                          DOMAINSEQS 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

   Add sequence records to a DCF file

2.0 INPUTS & OUTPUTS

   DOMAINSEQS parses a DCF file (domain classification file) and writes a
   file containing the same data, except that domain sequence information
   derived from structural and, optionally, sequence databases are added.
   Domain sequences are taken from domain CCF files (clean coordinate
   files) and (optionally) the swissprot database. If the swissprot
   sequence is used, DOMAINSEQS requires a swissprot:PDB equivalence file
   that gives the accession number of each PDB file corresponding to the
   domains in the DCF file. The path for the CCF files (input) and names
   of DCF files (input and output) are specified by the user. A log file
   is also written.

3.0 INPUT FILE FORMAT

   The format of the DCF file is described in the SCOPPARSE documentation.

  Input files for usage example

  File: ../scopparse-keep/all.scop

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   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//

  File: ../pdbtosp-domainatrix/Epdbtosp.dat

EN   101M
XX
NE   1
XX
IN   MYG_PHYCA ID; P02185 ACC;
XX
//
EN   102L
XX
NE   1
XX
IN   LYCV_BPT4 ID; P00720 ACC;
XX
//
EN   102M
XX
NE   1
XX
IN   MYG_PHYCA ID; P02185 ACC;
XX
//
EN   103L
XX
NE   1
XX
IN   LYCV_BPT4 ID; P00720 ACC;
XX
//
EN   103M
XX
NE   1
XX
IN   MYG_PHYCA ID; P02185 ACC;
XX
//
EN   9XIA
XX
NE   1
XX
IN   XYLA_STRRU ID; P24300 ACC;
XX
//
EN   9XIM
XX
NE   1
XX
IN   XYLA_ACTMI ID; P12851 ACC;
XX
//

4.0 OUTPUT FILE FORMAT

   The format of the DCF file is described in the SCOPPARSE documentation.
   DOMAINSEQS may add the following records:
     * (1) AC - Accession number of the domain sequence. This record will
       only be present if the DCF file has been processed using DOMAINSEQS
       and if an accession number for the PDB file corresponding to the
       domain is given in the swissprot:PDB equivalence file (generated by
       PDBTOSP) that DOMAINSEQS makes use of.
     * (2) SP - Swissprot code of the domain sequence. This record will
       only be present if the domain classification file has been
       processed using DOMAINSEQS and if an swissprot code for the PDB
       file corresponding to the domain is given in the swissprot:PDB
       equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use
       of.
     * (3) RA - Position of domain in swissprot sequence. The integers
       preceeding START and END give the start and end points respectively
       of the domain sequence relative to the full-length swissprot
       sequence.
     * (4) SQ - Sequence of the domain according to swissprot. This
       sequence is taken from the swissprot database. The SQ record will
       only be present if the SCOP classification file has been processed
       using DOMAINSEQS and if an accession number for the PDB file
       corresponding to the domain is given in the swissprot:PDB
       equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use
       of.

  Output files for usage example

  File: all_s.scop

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
DS   SEQUENCE    52 AA;   5817 MW;  D8CCAE0E1FC0849A CRC64;
     ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
DS   SEQUENCE    65 AA;   7395 MW;  75FBE75B22FD3678 CRC64;
     MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT
     LKKAI
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//

  File: domainseqs.log

//
D1CS4A_
NO_ACCESSION_NUMBER
//
D1II7A_
NO_ACCESSION_NUMBER

5.0 DATA FILES

   If the user specified retrieval of sequences from a sequence database,
   DOMAINSEQS uses a swissprot:PDB equivalence file is generated by using
   PDBTOSP.

6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

Add sequence records to 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.
  [-dpdbdir]           directory  [./] This option specifies the location of
                                  domain CCF file (clean coordinate files)
                                  (input). A 'clean cordinate file' contains
                                  coordinate and other data for a single PDB
                                  file or a single domain from SCOP or CATH,
                                  in CCF format (EMBL-like). The files,
                                  generated by using PDBPARSE (PDB files) or
                                  DOMAINER (domains), contain 'cleaned-up'
                                  data that is self-consistent and
                                  error-corrected. Records for residue solvent
                                  accessibility and secondary structure are
                                  added to the file by using PDBPLUS.
   -getswiss           toggle     [N] Retrieve swissprot sequence.
*  -pdbtospfile        infile     This option specifies the name of the
                                  pdbcodes to swissprot indexing file. The
                                  swissprot:PDB equivalence file is generated
                                  by PDBTOSP
  [-dcfoutfile]        outfile    [domainseqs.out] This option specifies the
                                  name of DCF file (domain classification
                                  file) (output). 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.
   -logfile            outfile    [domainseqs.log] This option specifies the
                                  name of log file for the build. The log file
                                  contains messages about any errors arising
                                  while domainseqs ran.

   Additional (Optional) qualifiers (* if not always prompted):
*  -datafile           matrixf    [EBLOSUM62] This option specifies the
                                  residue substitution matrix, which is used
                                  for sequence comparison.
*  -gapopen            float      [10.0 for any sequence] This option
                                  specifies the gap insertion penalty. This is
                                  the score taken away when a gap is created.
                                  The best value depends on the choice of
                                  comparison matrix. The default value assumes
                                  you are using the EBLOSUM62 matrix for
                                  protein sequences, and the EDNAFULL matrix
                                  for nucleotide sequences. (Floating point
                                  number from 1.0 to 100.0)
*  -gapextend          float      [0.5 for any sequence] This option specifies
                                  the gap extension penalty. This is added to
                                  the standard gap penalty for each base or
                                  residue in the gap. This is how long gaps
                                  are penalized. Usually you will expect a few
                                  long gaps rather than many short gaps, so
                                  the gap extension penalty should be lower
                                  than the gap penalty. (Floating point number
                                  from 0.0 to 10.0)

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

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

   "-dcfoutfile" associated qualifiers
   -odirectory3        string     Output directory

   "-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


