| ## DOMAINALIGN documentation

## CONTENTS

1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES

## 1.0 SUMMARY

Generate alignments (DAF file) for nodes in a DCF file

## 2.0 INPUTS & OUTPUTS

DOMAINALIGN generates a DAF file (domain alignment file) for each user-defined node (e.g. family or superfamily) in a DCF file (domain classification file) that is read. Each DAF file contains a structure-based sequence alignment annotated with domain classification data. If the STAMP algorithm is used, structural superimpositions are also generated and saved to file (PDB format). The alignments are calculated by using STAMP or TCOFFEE and these applications must be installed on the system that is running DOMAINALIGN (see 'Notes' below).
Clearly no alignment can be generated for nodes with a single entry (domain) only: sequences for such domains are (optionally) written to file (fasta format).
DOMAINALIGN requires a directory of domain PDB files; the path and extension of these must be set by the user (via the ACD file) and also specified in the STAMP "pdb.directories" file (see 'Notes' below)
A log file of diagnostic messages is written. The identifier (e.g SCOP Sunid) of the nodes from the DCF file are used to name the output files. The user also specifies the input file, paths for the two types of alignment files (output), path of singlet sequence files (if output) and name of log file.

## 3.0 INPUT FILE FORMAT

The format of the DCF (domain classification file) is described in SCOPPARSE documentation

### Input files for usage example

### File: all.scop2

    ID   D1CS4A_
    XX
    EN   1CS4
    XX
    TY   SCOP
    XX
    SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
    XX
    CL   Alpha and beta proteins (a+b)
    XX
    FO   Ferredoxin-like
    XX
    SF   Adenylyl and guanylyl cyclase catalytic domain
    XX
    FA   Adenylyl and guanylyl cyclase catalytic domain
    XX
    DO   Adenylyl cyclase VC1, domain C1a
    XX
    OS   Dog (Canis familiaris)
    XX
    NC   1
    XX
    CN   [1]
    XX
    CH   A CHAIN; . START; . END;
    //
    ID   D1FX2A_
    XX
    EN   1FX2
    XX
    TY   SCOP
    XX
    SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55081 DO; 55082 SO; 39430 DD;
    XX
    CL   Alpha and beta proteins (a+b)
    XX
    FO   Ferredoxin-like
    XX
    SF   Adenylyl and guanylyl cyclase catalytic domain
    XX
    FA   Adenylyl and guanylyl cyclase catalytic domain
    XX
    DO   Receptor-type monomeric adenylyl cyclase
    XX
    OS   Trypanosome (Trypanosoma brucei), different isoform
    XX
    NC   1
    XX
    CN   [1]
    XX

      [Part of this file has been deleted for brevity]

    XX
    EN   4AT1
    XX
    TY   SCOP
    XX
    SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39019 DD;
    XX
    CL   Alpha and beta proteins (a+b)
    XX
    FO   Ferredoxin-like
    XX
    SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
    XX
    FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
    XX
    DO   Aspartate carbamoyltransferase
    XX
    OS   Escherichia coli
    XX
    NC   1
    XX
    CN   [1]
    XX
    CH   B CHAIN; 8 START; 100 END;
    //
    ID   D4AT1D1
    XX
    EN   4AT1
    XX
    TY   SCOP
    XX
    SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39020 DD;
    XX
    CL   Alpha and beta proteins (a+b)
    XX
    FO   Ferredoxin-like
    XX
    SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
    XX
    FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
    XX
    DO   Aspartate carbamoyltransferase
    XX
    OS   Escherichia coli
    XX
    NC   1
    XX
    CN   [1]
    XX
    CH   D CHAIN; 8 START; 100 END;
    //

## 4.0 OUTPUT FILE FORMAT

Structure-based sequence alignment
The DAF (domain alignment file) format (Figure 1) consists of an alignment in EMBOSS "simple" multiple sequence alignment format with domain classification records. All lines other than sequence lines begin with '#' to denote a comment. The domain classification records for the appopriate node from the DCF file are given at the top of the file above the alignment. The records shown are TY (domain type, either SCOP or CATH), CL (class), FO (fold), SF (superfamily) and FA (family). For CATH domains, AR (architecture) and TP (topology) may also be given. Regardless of which node (family, superfamily etc) is represented, a unique identifier for the node is given after SI. Below the classification records, there are blocks that contain the sequence names, positions and aligned sequences. The names are the 7 character domain identifier codes taken from the DCF file. The positions are the start and end residue positions of the appropriate section of sequence. The sequence uses '-' as a gap character. The STAMP 'Post similar' line is given as a markup line underneath the sequence but no dssp assignments are written.

### Output files for usage example

### File: 54894.ent

    REMARK Output from transform
    REMARK  STAMP Package (Russell and Barton Proteins, 14, 309-323, 1992)
    REMARK Domains were read from the file ./domainalign-1234567890.1234.sort
    REMARK Chains are labelled sequentially starting with 'A' and
    REMARK  after the order given in the file ./domainalign-1234567890.1234.sort
    REMARK The domains in this file are:
    REMARK       d4at1b1  chain A
    REMARK       d4at1d1_1  chain B
    REMARK Does not include heteroatoms
    REMARK  Does not include DNA/RNA
    REMARK Does not include waters
    ATOM      1  N   GLY A   8      13.557  82.383  35.829  1.00 92.06           N
    ATOM      2  CA  GLY A   8      14.363  82.355  34.620  1.00 92.63           C
    ATOM      3  C   GLY A   8      14.480  83.797  34.150  1.00 91.80           C
    ATOM      4  O   GLY A   8      13.625  84.596  34.527  1.00 93.34           O
    ATOM      5  N   VAL A   9      15.499  84.132  33.352  1.00 90.04           N
    ATOM      6  CA  VAL A   9      15.799  85.525  33.008  1.00 89.55           C
    ATOM      7  C   VAL A   9      15.294  86.094  31.646  1.00 90.94           C
    ATOM      8  O   VAL A   9      14.395  85.528  31.008  1.00 91.46           O
    ATOM      9  CB  VAL A   9      17.381  85.731  33.167  1.00 88.13           C
    ATOM     10  CG1 VAL A   9      17.571  86.421  34.506  1.00 86.27           C
    ATOM     11  CG2 VAL A   9      18.232  84.456  33.191  1.00 86.95           C
    ATOM     12  N   GLU A  10      15.892  87.223  31.201  1.00 89.98           N
    ATOM     13  CA  GLU A  10      15.543  87.988  30.004  1.00 87.19           C
    ATOM     14  C   GLU A  10      16.748  88.251  29.055  1.00 83.25           C
    ATOM     15  O   GLU A  10      17.879  87.817  29.318  1.00 81.89           O
    ATOM     16  CB  GLU A  10      14.876  89.324  30.474  1.00 89.77           C
    ATOM     17  CG  GLU A  10      15.390  90.058  31.748  1.00 93.53           C
    ATOM     18  CD  GLU A  10      16.862  90.513  31.791  1.00 96.84           C
    ATOM     19  OE1 GLU A  10      17.570  90.129  32.731  1.00 98.75           O
    ATOM     20  OE2 GLU A  10      17.306  91.258  30.905  1.00 97.00           O
    ATOM     21  N   ALA A  11      16.471  89.023  27.987  1.00 77.76           N
    ATOM     22  CA  ALA A  11      17.315  89.379  26.829  1.00 71.32           C
    ATOM     23  C   ALA A  11      18.829  89.525  26.622  1.00 65.96           C
    ATOM     24  O   ALA A  11      19.605  90.124  27.370  1.00 64.35           O
    ATOM     25  CB  ALA A  11      16.692  90.608  26.193  1.00 70.48           C
    ATOM     26  N   ILE A  12      19.133  88.956  25.457  1.00 62.08           N
    ATOM     27  CA  ILE A  12      20.419  88.929  24.778  1.00 60.99           C
    ATOM     28  C   ILE A  12      19.984  89.116  23.325  1.00 61.87           C
    ATOM     29  O   ILE A  12      18.841  88.755  22.999  1.00 62.16           O
    ATOM     30  CB  ILE A  12      21.198  87.545  24.850  1.00 59.43           C
    ATOM     31  CG1 ILE A  12      20.354  86.363  24.347  1.00 55.38           C
    ATOM     32  CG2 ILE A  12      21.619  87.298  26.290  1.00 59.29           C
    ATOM     33  CD1 ILE A  12      21.107  85.072  24.029  1.00 50.25           C
    ATOM     34  N   LYS A  13      20.745  89.683  22.389  1.00 62.88           N
    ATOM     35  CA  LYS A  13      20.307  89.668  20.991  1.00 63.76           C
    ATOM     36  C   LYS A  13      21.229  88.611  20.439  1.00 63.26           C
    ATOM     37  O   LYS A  13      22.425  88.631  20.755  1.00 63.54           O
    ATOM     38  CB  LYS A  13      20.570  90.941  20.133  1.00 65.83           C
    ATOM     39  CG  LYS A  13      21.100  92.232  20.765  1.00 68.73           C

      [Part of this file has been deleted for brevity]

    ATOM    675  O   LYS B  94      12.694  74.659  17.436  1.00 60.00           O
    ATOM    676  CB  LYS B  94      11.414  76.090  20.144  1.00 54.56           C
    ATOM    677  CG  LYS B  94      10.901  77.252  20.962  1.00 56.83           C
    ATOM    678  CD  LYS B  94       9.923  76.671  21.990  1.00 59.11           C
    ATOM    679  CE  LYS B  94       9.043  77.717  22.641  1.00 60.10           C
    ATOM    680  NZ  LYS B  94       9.890  78.702  23.259  1.00 64.17           N
    ATOM    681  N   SER B  95      13.444  74.034  19.484  1.00 54.16           N
    ATOM    682  CA  SER B  95      13.785  72.651  19.195  1.00 49.80           C
    ATOM    683  C   SER B  95      13.767  71.904  20.531  1.00 49.50           C
    ATOM    684  O   SER B  95      13.715  72.494  21.617  1.00 50.66           O
    ATOM    685  CB  SER B  95      15.186  72.559  18.595  1.00 49.06           C
    ATOM    686  OG  SER B  95      15.488  73.550  17.615  1.00 48.30           O
    ATOM    687  N   ARG B  96      13.817  70.590  20.497  1.00 50.27           N
    ATOM    688  CA  ARG B  96      13.868  69.771  21.694  1.00 49.58           C
    ATOM    689  C   ARG B  96      14.839  68.647  21.295  1.00 47.31           C
    ATOM    690  O   ARG B  96      15.006  68.414  20.088  1.00 44.69           O
    ATOM    691  CB  ARG B  96      12.426  69.305  21.983  1.00 53.09           C
    ATOM    692  CG  ARG B  96      12.197  68.404  23.200  1.00 58.05           C
    ATOM    693  CD  ARG B  96      10.794  68.557  23.787  1.00 61.70           C
    ATOM    694  NE  ARG B  96      10.618  69.895  24.354  1.00 66.11           N
    ATOM    695  CZ  ARG B  96       9.772  70.814  23.850  1.00 69.37           C
    ATOM    696  NH1 ARG B  96       9.702  72.024  24.422  1.00 71.16           N
    ATOM    697  NH2 ARG B  96       8.988  70.558  22.790  1.00 70.99           N
    ATOM    698  N   PRO B  97      15.591  68.002  22.198  1.00 47.31           N
    ATOM    699  CA  PRO B  97      16.438  66.853  21.917  1.00 47.03           C
    ATOM    700  C   PRO B  97      15.755  65.610  21.357  1.00 46.69           C
    ATOM    701  O   PRO B  97      14.800  65.056  21.929  1.00 47.44           O
    ATOM    702  CB  PRO B  97      17.138  66.581  23.238  1.00 48.99           C
    ATOM    703  CG  PRO B  97      17.256  67.940  23.887  1.00 49.17           C
    ATOM    704  CD  PRO B  97      15.868  68.473  23.559  1.00 49.45           C
    ATOM    705  N   SER B  98      16.313  65.239  20.191  1.00 45.02           N
    ATOM    706  CA  SER B  98      16.016  64.022  19.436  1.00 41.65           C
    ATOM    707  C   SER B  98      17.197  63.101  19.711  1.00 39.46           C
    ATOM    708  O   SER B  98      18.327  63.608  19.718  1.00 38.78           O
    ATOM    709  CB  SER B  98      15.952  64.291  17.940  1.00 42.24           C
    ATOM    710  OG  SER B  98      14.657  64.744  17.586  1.00 46.01           O
    ATOM    711  N   LEU B  99      16.992  61.793  19.950  1.00 36.31           N
    ATOM    712  CA  LEU B  99      18.078  60.869  20.273  1.00 33.04           C
    ATOM    713  C   LEU B  99      19.004  60.692  19.051  1.00 33.65           C
    ATOM    714  O   LEU B  99      18.467  60.339  17.994  1.00 35.86           O
    ATOM    715  CB  LEU B  99      17.420  59.573  20.697  1.00 29.39           C
    ATOM    716  CG  LEU B  99      18.126  58.649  21.690  1.00 28.47           C
    ATOM    717  CD1 LEU B  99      18.261  59.352  23.048  1.00 27.24           C
    ATOM    718  CD2 LEU B  99      17.332  57.342  21.817  1.00 25.66           C
    ATOM    719  N   PRO B 100      20.325  60.971  19.041  1.00 33.12           N
    ATOM    720  CA  PRO B 100      21.146  60.885  17.830  1.00 35.17           C
    ATOM    721  C   PRO B 100      21.517  59.413  17.592  1.00 38.22           C
    ATOM    722  O   PRO B 100      21.547  58.620  18.542  1.00 36.98           O
    ATOM    723  CB  PRO B 100      22.317  61.776  18.143  1.00 34.28           C
    ATOM    724  CG  PRO B 100      22.530  61.464  19.626  1.00 33.62           C
    ATOM    725  CD  PRO B 100      21.124  61.360  20.204  1.00 31.93           C

### Directory: daf

This directory contains output files, for example 54894.daf and 55074.daf.

### File: daf/54894.daf

    # TY   SCOP
    # XX
    # CL   Alpha and beta proteins (a+b)
    # XX
    # FO   Ferredoxin-like
    # XX
    # SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
    # XX
    # FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
    # XX
    # SI   54894
    # XX
    #         Number               10        20        30        40        50
    d4at1b1              0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPXSGEMGRKDLIKIEN      0
    d4at1d1              0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGXEMGRKDLIKIEN      0
    # Post_similar         111111111111111111111111111111111111111111-0-111111111111

    #         Number        60        70        80        90
    d4at1b1              0 TFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP      0
    d4at1d1              0 TFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP      0
    # Post_similar         1111111111111111111111111111111111111

### File: daf/55074.daf

    # TY   SCOP
    # XX
    # CL   Alpha and beta proteins (a+b)
    # XX
    # FO   Ferredoxin-like
    # XX
    # SF   Adenylyl and guanylyl cyclase catalytic domain
    # XX
    # FA   Adenylyl and guanylyl cyclase catalytic domain
    # XX
    # SI   55074
    # XX
    #         Number               10        20        30        40        50
    d1cs4a_              0 MMFHKIYIQKXHXDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENH      0
    d1fx2a_              0 XXNNNRAPXKEPTDPVTLIFTDIESSTALWAAXHPDLMPDAVAAHHRMVRSLIGRYK      0
    # Post_similar         --000000-0-0-1111111111111111111-000111111111111111111111

    #         Number        60        70        80        90       100       110
    d1cs4a_              0 CLRIKILGDCYYCVSGLPEARADHAHCCVEMGMDMIEAISLVREMXTXGXXXXXXXX      0
    d1fx2a_              0 CYEVKTVGDSFMIAXXXXSKXXXSPFAAVQLAQELQLCFLHXHDWGTNALDDSYREF      0
    # Post_similar         11111111111111----00---111111111111111111-000-0-0--------

    #         Number          120       130       140       150       160       170
    d1cs4a_              0 XXXXXXXXXXXXXXXXXXXXXXXXXXXVNVNMRVGIHSGRVHXCGVLGLRKWQFDVW      0
    d1fx2a_              0 EEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIRHDXEXVTKGYDYY      0
    # Post_similar         ---------------------------011111111111111-111-0-00001111

    #         Number             180       190       200       210       220
    d1cs4a_              0 SNDVTLANHMEAGGKAGRIHITKATLSYLNXXXGXDYEVEPGCGGERNXAYLKEHSI      0
    d1fx2a_              0 GRTPNMAARTESVANGGQVLMTHAAYMSLSAEDRKQIDVTALXGDXVALRGXVSDPV      0
    # Post_similar         111111111111111111111111111111---0-1111111-00-00-00-00111

    #         Number      230       240       250
    d1cs4a_              0 ETFLILXXXXXXXXXXXXXXXXXX      0
    d1fx2a_              0 KMYQLNTVPSRNFAALRLDREYFD      0
    # Post_similar         111111------------------

### File: 55074.ent

    REMARK Output from transform
    REMARK  STAMP Package (Russell and Barton Proteins, 14, 309-323, 1992)
    REMARK Domains were read from the file ./domainalign-1234567890.1234.sort
    REMARK Chains are labelled sequentially starting with 'A' and
    REMARK  after the order given in the file ./domainalign-1234567890.1234.sort
    REMARK The domains in this file are:
    REMARK       d1cs4a_  chain A
    REMARK       d1fx2a__1  chain B
    REMARK Does not include heteroatoms
    REMARK  Does not include DNA/RNA
    REMARK Does not include waters
    ATOM      1  N   MET A 377      28.568 -27.770  32.255  1.00 73.77           N
    ATOM      2  CA  MET A 377      28.292 -26.443  32.794  1.00 72.28           C
    ATOM      3  C   MET A 377      29.325 -25.377  32.396  1.00 69.48           C
    ATOM      4  O   MET A 377      30.485 -25.687  32.098  1.00 67.04           O
    ATOM      5  CB  MET A 377      28.075 -26.504  34.312  1.00 74.79           C
    ATOM      6  CG  MET A 377      29.171 -27.205  35.092  1.00 78.73           C
    ATOM      7  SD  MET A 377      28.708 -27.446  36.824  1.00 83.74           S
    ATOM      8  CE  MET A 377      28.745 -25.745  37.440  1.00 81.94           C
    ATOM      9  N   MET A 378      28.883 -24.120  32.395  1.00 66.44           N
    ATOM     10  CA  MET A 378      29.698 -22.969  32.011  1.00 62.94           C
    ATOM     11  C   MET A 378      30.928 -22.727  32.886  1.00 59.70           C
    ATOM     12  O   MET A 378      32.059 -22.739  32.400  1.00 57.00           O
    ATOM     13  CB  MET A 378      28.824 -21.715  31.966  1.00 64.01           C
    ATOM     14  CG  MET A 378      27.551 -21.872  31.137  1.00 64.35           C
    ATOM     15  SD  MET A 378      27.897 -22.219  29.403  1.00 67.83           S
    ATOM     16  CE  MET A 378      27.844 -24.014  29.357  1.00 65.41           C
    ATOM     17  N   PHE A 379      30.697 -22.474  34.167  1.00 56.03           N
    ATOM     18  CA  PHE A 379      31.763 -22.225  35.123  1.00 53.16           C
    ATOM     19  C   PHE A 379      32.157 -23.501  35.837  1.00 51.53           C
    ATOM     20  O   PHE A 379      31.372 -24.440  35.914  1.00 53.09           O
    ATOM     21  CB  PHE A 379      31.296 -21.227  36.186  1.00 54.14           C
    ATOM     22  CG  PHE A 379      31.091 -19.832  35.671  1.00 51.13           C
    ATOM     23  CD1 PHE A 379      29.927 -19.493  34.986  1.00 50.12           C
    ATOM     24  CD2 PHE A 379      32.049 -18.846  35.907  1.00 49.63           C
    ATOM     25  CE1 PHE A 379      29.716 -18.196  34.546  1.00 51.63           C
    ATOM     26  CE2 PHE A 379      31.852 -17.545  35.474  1.00 50.16           C
    ATOM     27  CZ  PHE A 379      30.682 -17.216  34.792  1.00 51.72           C
    ATOM     28  N   HIS A 380      33.371 -23.529  36.372  1.00 50.09           N
    ATOM     29  CA  HIS A 380      33.830 -24.687  37.120  1.00 49.62           C
    ATOM     30  C   HIS A 380      33.046 -24.672  38.431  1.00 49.26           C
    ATOM     31  O   HIS A 380      32.579 -23.623  38.866  1.00 50.30           O
    ATOM     32  CB  HIS A 380      35.327 -24.574  37.439  1.00 52.29           C
    ATOM     33  CG  HIS A 380      36.235 -24.929  36.299  1.00 53.66           C
    ATOM     34  ND1 HIS A 380      36.782 -23.983  35.457  1.00 53.12           N
    ATOM     35  CD2 HIS A 380      36.737 -26.122  35.898  1.00 52.37           C
    ATOM     36  CE1 HIS A 380      37.581 -24.576  34.588  1.00 50.60           C
    ATOM     37  NE2 HIS A 380      37.572 -25.873  34.833  1.00 52.60           N
    ATOM     38  N   LYS A 381      32.879 -25.832  39.051  1.00 50.19           N
    ATOM     39  CA  LYS A 381      32.167 -25.897  40.318  1.00 51.93           C

      [Part of this file has been deleted for brevity]

    ATOM   1806  CG  ASP B1117      55.881   2.260  56.337  1.00 70.08           C
    ATOM   1807  OD1 ASP B1117      55.414   2.017  55.197  1.00 73.38           O
    ATOM   1808  OD2 ASP B1117      57.084   2.059  56.637  1.00 70.53           O
    ATOM   1809  N   ARG B1118      52.764   0.077  56.474  1.00 66.61           N
    ATOM   1810  CA  ARG B1118      52.481  -1.377  56.573  1.00 68.20           C
    ATOM   1811  C   ARG B1118      53.212  -2.511  55.828  1.00 68.77           C
    ATOM   1812  O   ARG B1118      54.421  -2.488  55.587  1.00 70.57           O
    ATOM   1813  CB  ARG B1118      51.033  -1.596  56.196  1.00 71.02           C
    ATOM   1814  CG  ARG B1118      49.988  -0.730  56.780  1.00 66.89           C
    ATOM   1815  CD  ARG B1118      48.805  -0.985  55.855  1.00 69.79           C
    ATOM   1816  NE  ARG B1118      47.548  -0.457  56.346  1.00 65.16           N
    ATOM   1817  CZ  ARG B1118      47.350   0.805  56.714  1.00 67.30           C
    ATOM   1818  NH1 ARG B1118      48.318   1.717  56.649  1.00 62.67           N
    ATOM   1819  NH2 ARG B1118      46.198   1.137  57.253  1.00 60.83           N
    ATOM   1820  N   GLU B1119      52.370  -3.490  55.468  1.00 74.62           N
    ATOM   1821  CA  GLU B1119      52.576  -4.775  54.756  1.00 71.44           C
    ATOM   1822  C   GLU B1119      51.216  -5.345  55.152  1.00 68.30           C
    ATOM   1823  O   GLU B1119      50.787  -5.071  56.255  1.00 70.28           O
    ATOM   1824  CB  GLU B1119      53.628  -5.683  55.451  1.00 72.63           C
    ATOM   1825  CG  GLU B1119      53.056  -6.991  56.217  1.00 68.78           C
    ATOM   1826  CD  GLU B1119      52.428  -6.728  57.622  1.00 67.37           C
    ATOM   1827  OE1 GLU B1119      52.888  -5.743  58.270  1.00 63.79           O
    ATOM   1828  OE2 GLU B1119      51.452  -7.444  58.067  1.00 24.30           O
    ATOM   1829  N   TYR B1120      50.504  -6.074  54.309  1.00 69.56           N
    ATOM   1830  CA  TYR B1120      49.237  -6.679  54.769  1.00 66.82           C
    ATOM   1831  C   TYR B1120      49.096  -7.992  54.006  1.00 69.41           C
    ATOM   1832  O   TYR B1120      49.547  -8.082  52.863  1.00 60.86           O
    ATOM   1833  CB  TYR B1120      48.062  -5.721  54.629  1.00 64.84           C
    ATOM   1834  CG  TYR B1120      46.960  -6.107  53.681  1.00 72.65           C
    ATOM   1835  CD1 TYR B1120      47.056  -5.809  52.324  1.00 69.04           C
    ATOM   1836  CD2 TYR B1120      45.764  -6.658  54.154  1.00 72.45           C
    ATOM   1837  CE1 TYR B1120      45.996  -6.038  51.461  1.00 74.31           C
    ATOM   1838  CE2 TYR B1120      44.688  -6.892  53.292  1.00 74.14           C
    ATOM   1839  CZ  TYR B1120      44.815  -6.576  51.947  1.00 77.01           C
    ATOM   1840  OH  TYR B1120      43.765  -6.791  51.087  1.00 73.74           O
    ATOM   1841  N   PHE B1121      48.537  -9.016  54.663  1.00 67.32           N
    ATOM   1842  CA  PHE B1121      48.401 -10.387  54.120  1.00 68.14           C
    ATOM   1843  C   PHE B1121      48.561 -10.745  52.626  1.00 68.72           C
    ATOM   1844  O   PHE B1121      49.618 -11.228  52.233  1.00 71.84           O
    ATOM   1845  CB  PHE B1121      47.210 -11.123  54.717  1.00 64.05           C
    ATOM   1846  CG  PHE B1121      47.408 -12.619  54.794  1.00 61.04           C
    ATOM   1847  CD1 PHE B1121      48.271 -13.164  55.734  1.00 58.84           C
    ATOM   1848  CD2 PHE B1121      46.737 -13.479  53.925  1.00 63.12           C
    ATOM   1849  CE1 PHE B1121      48.466 -14.540  55.815  1.00 60.74           C
    ATOM   1850  CE2 PHE B1121      46.925 -14.859  53.999  1.00 59.31           C
    ATOM   1851  CZ  PHE B1121      47.788 -15.392  54.941  1.00 64.18           C
    ATOM   1852  N   ASP B1122      47.527 -10.585  51.805  1.00 72.82           N
    ATOM   1853  CA  ASP B1122      47.656 -10.920  50.374  1.00 73.64           C
    ATOM   1854  C   ASP B1122      46.520 -10.365  49.515  1.00 74.17           C
    ATOM   1855  O   ASP B1122      46.464 -10.761  48.332  1.00 75.01           O
    ATOM   1856  CB  ASP B1122      47.790 -12.446  50.171  1.00 73.22           C

### File: domainalign.log

    Replaced ' ' in STAMP alignment with 'X'
    Replaced ' ' in STAMP alignment with 'X'
    Replaced ' ' in STAMP alignment with 'X'
    Replaced ' ' in STAMP alignment with 'X'
    Replaced ' ' in STAMP alignment with 'X'
    Replaced ' ' in STAMP alignment with 'X'
    Replaced ' ' in STAMP alignment with 'X'
    Replaced ' ' in STAMP alignment with 'X'
    Replaced ' ' in STAMP alignment with 'X'
    Replaced ' ' in STAMP alignment with 'X'
    Replaced ' ' in STAMP alignment with 'X'
    Replaced ' ' in STAMP alignment with 'X'
    Replaced ' ' in STAMP alignment with 'X'
    Replaced ' ' in STAMP alignment with 'X'

## 5.0 DATA FILES

DOMAINALIGN does not use any data files but uses the STAMP "pdb.directories" file which specifies the permissible prefix, extension and path of PDB files used by STAMP. This file should look like :

     test_data/ - .dent
     /data/pdb - -
     /data/pdb _ .ent
     /data/pdb _ .pdb
     /data/pdb pdb .ent
     /data/pdbscop _ _
     /data/pdbscop _ .ent
     /data/pdbscop _ .pdb
     /data/pdbscop pdb .ent
     ./ _ _
     ./ _ .ent
     ./ _ .ent.z
     ./ _ .ent.gz
     ./ _ .pdb
     ./ _ .pdb.Z
     ./ _ .pdb.gz
     ./ pdb .ent
     ./ pdb .ent.Z
     ./ pdb .ent.gz
     /data/CASS1/pdb/coords/ _ .pdb
     /data/CASS1/pdb/coords/ _ .pdb.Z
     /data/CASS1/pdb/coords/ _ .pdb.gz

## 6.0 USAGE

### 6.1 COMMAND LINE ARGUMENTS

    Generate alignments (DAF file) for nodes in a DCF file.
    Version: EMBOSS:6.6.0.0

       Standard (Mandatory) qualifiers (* if not always prompted):
      [-dcfinfile]         infile     This option specifies the name of DCF file
                                      (domain classification file) (input). A
                                      'domain classification file' contains
                                      classification and other data for domains
                                      from SCOP or CATH, in DCF format
                                      (EMBL-like). The files are generated by
                                      using SCOPPARSE and CATHPARSE. Domain
                                      sequence information can be added to the
                                      file by using DOMAINSEQS.
      [-pdbdir]            directory  [./] This option specifies the location of
                                      domain PDB files (input). A 'domain PDB
                                      file' contains coordinate data for a single
                                      domain from SCOP or CATH, in PDB format. The
                                      files are generated by using DOMAINER.
       -node               menu       [1] This option specifies the node for
                                      redundancy removal. Redundancy can be
                                      removed at any specified node in the SCOP or
                                      CATH hierarchies. For example by selecting
                                      'Class' entries belonging to the same Class
                                      will be non-redundant. (Values: 1 (Class
                                      (SCOP)); 2 (Fold (SCOP)); 3 (Superfamily
                                      (SCOP)); 4 (Family (SCOP)); 5 (Class
                                      (CATH)); 6 (Architecture (CATH)); 7
                                      (Topology (CATH)); 8 (Homologous Superfamily
                                      (CATH)); 9 (Family (CATH)))
       -mode               menu       [1] This option specifies the alignment
                                      algorithm to use. (Values: 1 (STAMP); 2
                                      (TCOFFEE))
       -[no]keepsinglets   toggle     [Y] This option specifies whether to write
                                      sequences of singlet families to file. If
                                      you specify this option, the sequence for
                                      each singlet family are written to file
                                      (output).
      [-dafoutdir]         outdir     [./] This option specifies the location of
                                      DAF files (domain alignment files) (output).
                                      A 'domain alignment file' contains a
                                      sequence alignment of domains belonging to
                                      the same SCOP or CATH family. The files are
                                      in clustal format and are annotated with
                                      domain family classification information.
                                      The files generated by using SCOPALIGN will
                                      contain a structure-based sequence alignment
                                      of domains of known structure only. Such
                                      alignments can be extended with sequence
                                      relatives (of unknown structure) by using
                                      SEQALIGN.
    *  -singletsoutdir     outdir     [./] This option specifies the location of
                                      DHF files (domain hits files) for singlet
                                      sequences (output). The singlets are written
                                      out as a 'domain hits file' - which
                                      contains database hits (sequences) with
                                      domain classification information, in FASTA
                                      format.
    *  -superoutdir        outdir     [./] This option specifies the location of
                                      structural superimposition files (output). A
                                      file in PDB format of the structural
                                      superimposition is generated for each family
                                      if the STAMP algorithm is used.
       -logfile            outfile    [domainalign.log] This option specifies the
                                      name of log file (output). The log file
                                      contains messages about any errors arising
                                      while domainalign ran.

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-pdbdir" associated qualifiers
       -extension2         string     Default file extension

       "-dafoutdir" associated qualifiers
       -extension3         string     Default file extension

       "-singletsoutdir" associated qualifiers
       -extension          string     Default file extension

       "-superoutdir" associated qualifiers
       -extension          string     Default file extension

       "-logfile" associated qualifiers
       -odirectory         string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options and exit. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-dcfinfile] (Parameter 1) | infile | This option specifies the name of DCF file (domain classification file) (input). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. | Input file | Required
[-pdbdir] (Parameter 2) | directory | This option specifies the location of domain PDB files (input). A 'domain PDB file' contains coordinate data for a single domain from SCOP or CATH, in PDB format. The files are generated by using DOMAINER. | Directory | ./
-node | list | This option specifies the node for redundancy removal. Redundancy can be removed at any specified node in the SCOP or CATH hierarchies. For example by selecting 'Class' entries belonging to the same Class will be non-redundant. |
1 | (Class (SCOP))
2 | (Fold (SCOP))
3 | (Superfamily (SCOP))
4 | (Family (SCOP))
5 | (Class (CATH))
6 | (Architecture (CATH))
7 | (Topology (CATH))
8 | (Homologous Superfamily (CATH))
9 | (Family (CATH))
| 1
-mode | list | This option specifies the alignment algorithm to use. |
1 | (STAMP)
2 | (TCOFFEE)
| 1
-[no]keepsinglets | toggle | This option specifies whether to write sequences of singlet families to file. If you specify this option, the sequence for each singlet family are written to file (output). | Toggle value Yes/No | Yes
[-dafoutdir] (Parameter 3) | outdir | This option specifies the location of DAF files (domain alignment files) (output). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The files are in clustal format and are annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. | Output directory | ./
-singletsoutdir | outdir | This option specifies the location of DHF files (domain hits files) for singlet sequences (output). The singlets are written out as a 'domain hits file' - which contains database hits (sequences) with domain classification information, in FASTA format. | Output directory | ./
-superoutdir | outdir | This option specifies the location of structural superimposition files (output). A file in PDB format of the structural superimposition is generated for each family if the STAMP algorithm is used. | Output directory | ./
-logfile | outfile | This option specifies the name of log file (output). The log file contains messages about any errors arising while domainalign ran. | Output file | domainalign.log
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-pdbdir" associated directory qualifiers
-extension2 -extension_pdbdir | string | Default file extension | Any string | ent
"-dafoutdir" associated outdir qualifiers
-extension3 -extension_dafoutdir | string | Default file extension | Any string | daf
"-singletsoutdir" associated outdir qualifiers
-extension | string | Default file extension | Any string | dhf
"-superoutdir" associated outdir qualifiers
-extension | string | Default file extension | Any string | ent
"-logfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

### 6.2 EXAMPLE SESSION

An example of interactive use of DOMAINALIGN is shown below. Here is a sample session with domainalign

    % domainalign
    Generate alignments (DAF file) for nodes in a DCF file.
    Domain classification file: all.scop2
    Domain pdb directory [./]:
    Node at which to remove redundancy
             1 : Class (SCOP)
             2 : Fold (SCOP)
             3 : Superfamily (SCOP)
             4 : Family (SCOP)
             5 : Class (CATH)
             6 : Architecture (CATH)
             7 : Topology (CATH)
             8 : Homologous Superfamily (CATH)
             9 : Family (CATH)
    Select number. [1]: 4
    Alignment algorithm option
             1 : STAMP
             2 : TCOFFEE
    Select number. [1]: 1
    Write sequences of singlet families to file. [Y]: N
    Domain alignment file output directory [./]: daf
    Pdb entry file output directory [./]:
    Domainatrix log output file [domainalign.log]:

    STAMP Structural Alignment of Multiple Proteins
     by Robert B. Russell & Geoffrey J. Barton
     Please cite PROTEINS, v14, 309-323, 1992

    Results of scan will be written to file ./domainalign-1234567890.1234.scan
    Fits  = no. of fits performed, Sc = STAMP score, RMS = RMS deviation
    Align = alignment length, Nfit = residues fitted, Eq. = equivalent residues
    Secs  = no. equiv. secondary structures, %I = seq. identity, %S = sec. str. identity
    P(m)  = P value (p=1/10) calculated after Murzin (1993), JMB, 230, 689-694

         Domain1         Domain2          Fits  Sc      RMS   Len1 Len2 Align Fit   Eq. Secs    %I    %S     P(m)
    Scan d1cs4a_         d1cs4a_            1   9.799   0.001  189  189  189  189  188    0 100.00 100.00 0.00e+00
    Scan d1cs4a_         d1fx2a_            1   6.522   1.343  189  235  225  135  133    0  20.30 100.00 0.00017
    See the file ./domainalign-1234567890.1234.scan

    /shared/software/bin/stamp -l ./domainalign-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainalign-1234567890.1234 -d ./domainalign-1234567890.1234.set

    /shared/software/bin/sorttrans -f ./domainalign-1234567890.1234.scan -s Sc 2.5 > ./domainalign-1234567890.1234.sort

    /shared/software/bin/stamp -l ./domainalign-1234567890.1234.sort -prefix ./domainalign-1234567890.1234 > ./domainalign-1234567890.1234.log

    TRANSFORM R.B. Russell, 1995
     Using PDB files
     Files will not include heteroatoms
     Files will not include DNA/RNA
     Files will not include waters
     All coordinates will be in file ./55074.ent
     Domain   1, d1cs4a_ => to ./55074.ent (chain A)
     Domain   2, d1fx2a__1 => to ./55074.ent (chain B)
    POSTSTAMP, R.B. Russell 1995
     New output will be in file ./domainalign-1234567890.1234.1
     E1 =   3.800, E2 =   3.800
     Minimum Pij set to 0.500
     Reading domain descriptors/transformations from the file ./domainalign-1234567890.1234.1
     Reading alignment...
      Reading coordinates...
     Domain   1 /homes/user/test/qa/domainer-keep2//d1cs4a_.ent d1cs4a_
            all residues 189 CAs =>  189 CAs in total
     Transforming coordinates...
     Domain   2 /homes/user/test/qa/domainer-keep2//d1fx2a_.ent d1fx2a__1
            all residues 235 CAs =>  235 CAs in total
     Transforming coordinates...
     ...done.

    /shared/software/bin/transform -f ./domainalign-1234567890.1234.sort -g  -o ./55074.ent

    /shared/software/bin/poststamp -f ./domainalign-1234567890.1234.1 -min 0.5

    /shared/software/bin/ver2hor -f ./domainalign-1234567890.1234.1.post > ./domainalign-1234567890.1234.out

    STAMP Structural Alignment of Multiple Proteins
     by Robert B. Russell & Geoffrey J. Barton
     Please cite PROTEINS, v14, 309-323, 1992

    Results of scan will be written to file ./domainalign-1234567890.1234.scan
    Fits  = no. of fits performed, Sc = STAMP score, RMS = RMS deviation
    Align = alignment length, Nfit = residues fitted, Eq. = equivalent residues
    Secs  = no. equiv. secondary structures, %I = seq. identity, %S = sec. str. identity
    P(m)  = P value (p=1/10) calculated after Murzin (1993), JMB, 230, 689-694

         Domain1         Domain2          Fits  Sc      RMS   Len1 Len2 Align Fit   Eq. Secs    %I    %S     P(m)
    Scan d4at1b1         d4at1b1            1   9.799   0.001   93   93   93   93   92    0 100.00 100.00 1.00e-92
    Scan d4at1b1         d4at1d1            1   9.251   0.588   93   93   94   89   88    0 100.00 100.00 1.00e-88
    See the file ./domainalign-1234567890.1234.scan

    Processing node 54894

    /shared/software/bin/stamp -l ./domainalign-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainalign-1234567890.1234 -d ./domainalign-1234567890.1234.set

    /shared/software/bin/sorttrans -f ./domainalign-1234567890.1234.scan -s Sc 2.5 > ./domainalign-1234567890.1234.sort

    /shared/software/bin/stamp -l ./domainalign-1234567890.1234.sort -prefix ./domainalign-1234567890.1234 > ./domainalign-1234567890.1234.log

    TRANSFORM R.B. Russell, 1995
     Using PDB files
     Files will not include heteroatoms
     Files will not include DNA/RNA
     Files will not include waters
     All coordinates will be in file ./54894.ent
     Domain   1, d4at1b1 => to ./54894.ent (chain A)
     Domain   2, d4at1d1_1 => to ./54894.ent (chain B)
    POSTSTAMP, R.B. Russell 1995
     New output will be in file ./domainalign-1234567890.1234.1
     E1 =   3.800, E2 =   3.800
     Minimum Pij set to 0.500
     Reading domain descriptors/transformations from the file ./domainalign-1234567890.1234.1
     Reading alignment...
      Reading coordinates...
     Domain   1 /homes/user/test/qa/domainer-keep2//d4at1b1.ent d4at1b1
            all residues  93 CAs =>   93 CAs in total
     Transforming coordinates...
     Domain   2 /homes/user/test/qa/domainer-keep2//d4at1d1.ent d4at1d1_1
            all residues  93 CAs =>   93 CAs in total
     Transforming coordinates...
     ...done.

    /shared/software/bin/transform -f ./domainalign-1234567890.1234.sort -g  -o ./54894.ent

    /shared/software/bin/poststamp -f ./domainalign-1234567890.1234.1 -min 0.5

    /shared/software/bin/ver2hor -f ./domainalign-1234567890.1234.1.post > ./domainalign-1234567890.1234.out

Go to the input files for this example
Go to the output files for this example

The following command line would achieve the same result.

     domainalign /test_data/all.scop2 /test_data/ /test_data/ /test_data/domainalign -keepsinglets Y
    -singlets /test_data/domainalign -node 4 -mode 1

-->

## 7.0 KNOWN BUGS & WARNINGS

1. Use of stamp
DOMAINALIGN requires a modified version of STAMP (see Notes below). The modified STAMP application must be installed on the system that is running DOMAINALIGN.
2. Strange STAMP behaviour
STAMP will ignore (omit from the alignment and *not* replace with '-' or any other symbol) ANY residues or groups in a PDB file that
(i) are not structured (i.e. do not appear in the ATOM records) or
(ii) lack a CA atom, regardless of whether it is a known amino acid or not.
This means that the position (column) in the alignment cannot reliably be used as the basis for an index into arrays representing the full length sequences. STAMP will however include in the alignment residues with a single atom only, so long as it is the CA atom.
3. Handling of singlet nodes
No sequence alignment or structural superimposition files are generated for nodes that contain a single domain only. Sequences for such domains can be saved to file (see 2.0 INPUTS & OUTPUTS).
4. Alignment numbering
Residue number positions in alignment are not implemented (zero's are given).

## 8.0 NOTES

1. Adaption of STAMP for domain codes
DOMAINALIGN will only run with with a version of STAMP which has been modified so that PDB id codes of length greater than 4 characters are acceptable. This involves a trivial change to the STAMP module getdomain.c (around line number 155), a 4 must be changed to a 7 as follows:

     temp=getfile(domain[0].id,dirfile,4,OUTPUT);
     temp=getfile(domain[0].id,dirfile,7,OUTPUT);

2. Adaption of STAMP for larger datasets
STAMP fails to align a large dataset of all the available V set Ig domains. The ver2hor module generates the following error:

     Transforming coordinates...
      ...done.
     ver2hor -f ./domainalign-1022069396.11280.76.post > ./domainalign-1022069396.11280.out
     error: something wrong with STAMP file
              STAMP length is 370, Alignment length is 422
              STAMP nseq is 155, Alignment nseq is 155

This is fixed by the following change in alignfit.h.

    #define MAXtlen 200
    #define MAXtlen 2000

At the same time the following may be changed as a safety measure:

     gstamp.c  : #define MAX_SEQ_LEN 10000    (was 2000)
     pdbseq.c  : #define MAX_SEQ_LEN 10000    (was 3000)
     defaults.h: #define MAX_SEQ_LEN 10000    (was 8000)
     defaults.h: #define MAX_NSEQ 10000       (was 1000)
     defaults.h: #define MAX_BLOC_SEQ 5000    (was 500)
     dstamp.h  : #define MAX_N_SEQ 10000      (was 1000)
     ver2hor.h : #define MAX_N_SEQ 10000      (was 1000)

3. pdb.directories file
STAMP (and therefore DOMAINALIGN) uses a "pdb.directories" file: see 5.0 DATA FILES
4. Choice of alignment algorithm
Future versions of DOMAINALIGN will implement a larger choice of alignment algorithms.
5. Getting the best alignment
DOMAINALIGN will produce better alignments if the DCF file is reordered so that the representative structure of each node (e.g. family) is given first. This is achieved by using DOMAINREP.
6. Whitespace in alignment
STAMP can insert non-sensical whitespaces into its alignments, e.g. instead of a residue character where that residue was missing electron density in the PDB file. DOMAINALIGN replaces each whitespace within a STAMP alignment with an "X".

### 8.1 GLOSSARY OF FILE TYPES

FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO
Domain classification file (for SCOP) | DCF format (EMBL-like format for domain classification data). | Classification and other data for domains from SCOP. | SCOPPARSE | Domain sequence information can be added to the file by using DOMAINSEQS.
Domain classification file (for CATH) | DCF format (EMBL-like format for domain classification data). | Classification and other data for domains from CATH. | CATHPARSE | Domain sequence information can be added to the file by using DOMAINSEQS.
Domain PDB file | PDB format for domain coordinate data. | Coordinate data for a single domain from SCOP or CATH. | DOMAINER | N.A.
Domain alignment file | DAF format (clustal format with domain classification information). | Contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is annotated with domain family classification information. | DOMAINALIGN (structure-based sequence alignment of domains of known structure). | DOMAINALIGN alignments can be extended with sequence relatives (of unknown structure) to the family in question by using SEQALIGN.

None

## 9.0 DESCRIPTION

The generation of alignments for large datasets such as SCOP and CATH potentially requires a lot of time for preparation of datasets, writing of scripts, running individual jobs and so on, in addition to the compute time required for the alignments themselves. DOMAINALIGN automates this process: it reads a domain classification file and generates alignments for each user-specified node in turn.

## 10.0 ALGORITHM

More information on STAMP can be found at http://www.compbio.dundee.ac.uk/manuals/stamp.4.2
More information on TCOFFEE can be found at http://www.ch.embnet.org/software/TCoffee.html

## 11.0 RELATED APPLICATIONS

## See also

Program name | Description
--- | ---
cathparse | Generate DCF file from raw CATH files
domainnr | Remove redundant domains from a DCF file
domainrep | Reorder DCF file to identify representative structures
domainseqs | Add sequence records to a DCF file
domainsse | Add secondary structure records to a DCF file
helixturnhelix | Identify nucleic acid-binding motifs in protein sequences
libgen | Generate discriminating elements from alignments
matcher | Waterman-Eggert local alignment of two sequences
matgen3d | Generate a 3D-1D scoring matrix from CCF files
oalistat | Statistics for multiple alignment files
pepcoil | Predict coiled coil regions in protein sequences
rocon | Generate a hits file from comparing two DHF files
rocplot | Perform ROC analysis on hits files
scopparse | Generate DCF file from raw SCOP files
seqalign | Extend alignments (DAF file) with sequences (DHF file)
seqfraggle | Remove fragment sequences from DHF files
seqmatchall | All-against-all word comparison of a sequence set
seqsort | Remove ambiguous classified sequences from DHF files
seqwords | Generate DHF files from keyword search of UniProt
ssematch | Search a DCF file for secondary structure matches
supermatcher | Calculate approximate local pair-wise alignments of larger sequences
water | Smith-Waterman local alignment of sequences
wordfinder | Match large sequences against one or more other sequences
wordmatch | Find regions of identity (exact matches) of two sequences

## 12.0 DIAGNOSTIC ERROR MESSAGES

The following message may appear in the log file.
Replaced ' ' in STAMP alignment with 'X' (STAMP can insert non-sensical whitespaces into its alignments, e.g. instead of a residue character where that residue was missing electron density in the PDB file. DOMAINALIGN replaces each whitespace within a STAMP alignment with an "X").

## 13.0 AUTHORS

Ranjeeva Ranasinghe
Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK

## 14.0 REFERENCES

Please cite the authors and EMBOSS.
Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

See also http://emboss.sourceforge.net/

### 14.1 Other useful references

Russell, R. B. & Barton, G. J. (1992), Multiple Sequence Alignment from Tertiary Structure Comparison: Assignment of Global and Residue Confidence Levels, PROTEINS: Struct. Funct. Genet., 14, 309-323.
C. Notredame, D. Higgins, J. Heringa. T-Coffee: A novel method for multiple sequence alignments. Journal of Molecular Biology, 302, 205-217, (2000)
More information on STAMP can be found at http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/
More information on TCOFFEE can be found at http://www.ch.embnet.org/software/TCoffee.html