| ## SEQWORDS 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

Generates DHF files (domain hits files) of database hits (sequences) from Swissprot matching keywords from a keywords file. Generate DHF files from keyword search of UniProt

## 2.0 INPUTS & OUTPUTS

SEQWORDS searches a swissprot-format sequence database with keywords taken from a keywords file, and writes a DHF file (domain hits file) of sequences whose swissprot entries contains at least one of the keywords. If an entry contains a keyword in a domain record of the feature table, then the sequence of the domain is written to the output file, otherwise the entire sequence is written. The user specifies the name of the swissprot-format sequence database (input), keywords file (input) and DHF file (output).

## 3.0 INPUT FILE FORMAT

The keywords file (below) contains lists of keywords specific to a number of SCOP or CATH nodes, e.g. families and superfamilies. Each list of keywords is given after a block of SCOP or CATH classification records; for family-specific search terms, the block must contain a CL, FO, SF and an FA record (see below). For superfamily-specific terms, clearly only the CL, FO and SF should be specified. A single keyword must be given per line after the record 'TE'. Each block of SCOP or CATH classification records and search terms must be delimited by the record '//' (the file should also end with this record).
It is possible to provide search terms above the level of superfamily, for example, fold and class-specific search terms for SCOP by using the CL and FO records only as appropriate. However, text searches of swissprot for members of scop folds and classes are unlikely to produce specific or meaningful results.

### Input files for usage example

### File: seqwords.terms

    TY   SCOP
    XX
    CL   Alpha and beta proteins (a/b)
    XX
    FO   NAD(P)-binding Rossmann-fold domains
    XX
    SF   NAD(P)-binding Rossmann-fold domains
    XX
    FA   Lactate & malate dehydrogenases, N-terminal domain
    XX
    TE   NAD(P)-binding Rossmann-fold
    TE   Lactate & malate dehydrogenases
    TE   Lactate dehydrogenase
    TE   Malate dehydrogenase
    //

### File: seqwords.seq

    ID   ACEA_ECOLI     STANDARD;      PRT;   434 AA.
    AC   P05313;
    DT   01-NOV-1988 (Rel. 09, Created)
    DT   01-NOV-1988 (Rel. 09, Last sequence update)
    DT   15-DEC-1998 (Rel. 37, Last annotation update)
    DE   ISOCITRATE LYASE (EC 4.1.3.1) (ISOCITRASE) (ISOCITRATASE) (ICL).
    GN   ACEA OR ICL.
    OS   Escherichia coli.
    OC   Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
    OC   Escherichia.
    RN   [1]
    RP   SEQUENCE FROM N.A.
    RC   STRAIN=K12;
    RX   MEDLINE; 89083515.
    RA   Byrne C.R., Stokes H.W., Ward K.A.;
    RT   "Nucleotide sequence of the aceB gene encoding malate synthase A in
    RT   Escherichia coli.";
    RL   Nucleic Acids Res. 16:10924-10924(1988).
    RN   [2]
    RP   SEQUENCE FROM N.A.
    RC   STRAIN=K12;
    RX   MEDLINE; 88262573.
    RA   Rieul C., Bleicher F., Duclos B., Cortay J.-C., Cozzone A.J.;
    RT   "Nucleotide sequence of the aceA gene coding for isocitrate lyase in
    RT   Escherichia coli.";
    RL   Nucleic Acids Res. 16:5689-5689(1988).
    RN   [3]
    RP   SEQUENCE FROM N.A.
    RX   MEDLINE; 89008064.
    RA   Matsuoka M., McFadden B.A.;
    RT   "Isolation, hyperexpression, and sequencing of the aceA gene encoding
    RT   isocitrate lyase in Escherichia coli.";
    RL   J. Bacteriol. 170:4528-4536(1988).
    RN   [4]
    RP   SEQUENCE FROM N.A.
    RC   STRAIN=K12 / MG1655;
    RX   MEDLINE; 94089392.
    RA   Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J.,
    RA   Daniels D.L.;
    RT   "Analysis of the Escherichia coli genome. IV. DNA sequence of the
    RT   region from 89.2 to 92.8 minutes.";
    RL   Nucleic Acids Res. 21:5408-5417(1993).
    RN   [5]
    RP   SEQUENCE OF 293-434 FROM N.A.
    RX   MEDLINE; 88227861.
    RA   Klumpp D.J., Plank D.W., Bowdin L.J., Stueland C.S., Chung T.,
    RA   Laporte D.C.;
    RT   "Nucleotide sequence of aceK, the gene encoding isocitrate
    RT   dehydrogenase kinase/phosphatase.";
    RL   J. Bacteriol. 170:2763-2769(1988).

      [Part of this file has been deleted for brevity]

    FT   CONFLICT     70     70       A -> R (IN REF. 2).
    FT   CONFLICT     80     80       A -> R (IN REF. 1 AND 2).
    FT   CONFLICT    116    116       I -> N (IN REF. 2).
    FT   CONFLICT    144    144       F -> L (IN REF. 1).
    FT   CONFLICT    305    312       LGEEFVNK -> WAKSSLISN (IN REF. 2).
    FT   CONFLICT    307    307       E -> Q (IN REF. 1).
    FT   STRAND        2      6
    FT   TURN          7      9
    FT   HELIX        11     23
    FT   TURN         26     27
    FT   STRAND       28     33
    FT   TURN         37     38
    FT   HELIX        39     47
    FT   TURN         48     48
    FT   STRAND       53     58
    FT   HELIX        64     67
    FT   TURN         68     69
    FT   STRAND       72     75
    FT   TURN         83     84
    FT   HELIX        87    108
    FT   TURN        110    111
    FT   STRAND      113    116
    FT   HELIX       121    134
    FT   TURN        135    136
    FT   TURN        140    141
    FT   STRAND      143    145
    FT   HELIX       148    162
    FT   TURN        163    163
    FT   HELIX       166    168
    FT   STRAND      173    175
    FT   TURN        179    181
    FT   STRAND      182    184
    FT   HELIX       186    188
    FT   TURN        190    191
    FT   HELIX       196    217
    FT   TURN        218    219
    FT   HELIX       225    242
    FT   TURN        243    244
    FT   STRAND      248    255
    FT   STRAND      263    271
    FT   TURN        272    273
    FT   STRAND      274    278
    FT   HELIX       286    311
    SQ   SEQUENCE   312 AA;  32337 MW;  17741A3B5AD068BA CRC64;
         MKVAVLGAAG GIGQALALLL KTQLPSGSEL SLYDIAPVTP GVAVDLSHIP TAVKIKGFSG
         EDATPALEGA DVVLISAGVA RKPGMDRSDL FNVNAGIVKN LVQQVAKTCP KACIGIITNP
         VNTTVAIAAE VLKKAGVYDK NKLFGVTTLD IIRSNTFVAE LKGKQPGEVE VPVIGGHSGV
         TILPLLSQVP GVSFTEQEVA DLTKRIQNAG TEVVEAKAGG GSATLSMGQA AARFGLSLVR
         ALQGEQGVVE CAYVEGDGQY ARFFSQPLLL GKNGVEERKS IGTLSAFEQN ALEGMLDTLK
         KDIALGEEFV NK
    //

## 4.0 OUTPUT FILE FORMAT

DHF file (domain hits file)
The format of the DHF file (domain hits file) of hit sequences generated by SEQWORDS (Figure 1) is described fully in SEQSEARCH documentation and only summarised here. The file contains two lines per hit, the first is a description of the hit in 16 text tokens delimited by '^'. The second line contains the protein sequence. The first 4 tokens refer to the hit (sequence) itself, the tokens are as follows:

- (i) Accession number
- (ii) Database code,
- (iii - iv) Start and end positions of the hit relative to the full length sequence.

The next 9 tokens refer to the domain family, superfamily etc for which the terms were defined (in the keywords file) and are as follows:

- (v) Type of domain (one of 'SCOP' or 'CATH'),
- (vi) SCOP or CATH domain identifier.
- (vii) SCOP or CATH node unique identifier, e.g. SCOP Family Sunid.
- (viii) Domain class. Textual description of the 'Class' (SCOP and CATH domains).
- (ix) Domain architecture. Textual description of the 'Architecture' (CATH only).
- (x) Domain topology. Textual description of the 'Topology' (CATH only).
- (xi) Domain fold. Textual description of the 'Fold' (SCOP domains only).
- (xii) Domain superfamily. Textual description of the 'Superfamily' (SCOP and CATH domains).
- (xiii) Domain family. Textual description of the 'Fold' (SCOP only).

The next 4 tokens refer to the hit, specifically, information about the search result as follows:

- (xiv) Model type. The type of model that was used to generate the hit. For DHF files generated by using SEQWORDS a value of KEYWORD is given. Several other values are possible, however, see SEQSEARCH documentation.
- (xv) SC - Score of hit from search algoritm (not written by SEQWORDS).
- (xvi) P-value of hit (not written by SEQWORDS).
- (xvii) E-value of hit (not written by SEQWORDS).

### Output files for usage example

### File: seqwords.dhf

    > Q60150^.^1^312^SCOP^.^0^Alpha and beta proteins (a/b)^.^.^NAD(P)-binding Rossmann-fold domains^NAD(P)-binding Rossmann-fold domains^Lactate & malate dehydrogenases, N-terminal domain^KEYWORD^0.00^0.000e+00^0.000e+00
    MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGEDATPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVQQVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDIIRSNTFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQVPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVECAYVEGDGQYARFFSQPLLLGKNGVEERKSIGTLSAFEQNALEGMLDTLKKDIALGEEFVNK

## 5.0 DATA FILES

SEQWORDS does not use a data file.

## 6.0 USAGE

    Generate DHF files from keyword search of UniProt.
    Version: EMBOSS:6.6.0.0

       Standard (Mandatory) qualifiers:
      [-keyfile]           infile     This option specifies the name of keywords
                                      file (input). This contains a list of
                                      keywords specific to a number of SCOP or
                                      CATH families and superfamilies used by
                                      SEQWORDS to search a sequence database.
      [-spfile]            infile     This option specifies the name of the
                                      sequence database (input) to search.
      [-outfile]           outfile    [test.hits] This option specifies the name
                                      of the DHF file (domain hits file) (output).
                                      A 'domain hits file' contains database hits
                                      (sequences) with domain classification
                                      information, in the DHF format (FASTA-like).
                                      The hits are relatives to a SCOP or CATH
                                      family (or other node in the structural
                                      hierarchies) and are found from a search of
                                      a sequence database. Files containing hits
                                      retrieved by PSIBLAST are generated by using
                                      SEQSEARCH, hits retrieved by a sparse
                                      protein signatare by using SIGSCAN or
                                      various types of HMM and profile by using
                                      LIBSCAN.

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

       "-outfile" associated qualifiers
       -odirectory3        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

### 6.1 COMMAND LINE ARGUMENTS

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-keyfile] (Parameter 1) | infile | This option specifies the name of keywords file (input). This contains a list of keywords specific to a number of SCOP or CATH families and superfamilies used by SEQWORDS to search a sequence database. | Input file | Required
[-spfile] (Parameter 2) | infile | This option specifies the name of the sequence database (input) to search. | Input file | Required
[-outfile] (Parameter 3) | outfile | This option specifies the name of the DHF file (domain hits file) (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA-like). The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH, hits retrieved by a sparse protein signatare by using SIGSCAN or various types of HMM and profile by using LIBSCAN. | Output file | test.hits
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory3 -odirectory_outfile | 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 SEQWORDS is shown below. Here is a sample session with seqwords

    % seqwords
    Generate DHF files from keyword search of UniProt.
    Keywords file: seqwords.terms
    Swissprot-format database file: seqwords.seq
    Domain hits output file [test.hits]: seqwords.dhf

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

## 7.0 KNOWN BUGS & WARNINGS

SEQWORDS is slow - swissprot is read multiple times (once for each list of terms). Changing it to do a single file read would require modifying the program to take an array of hitlist and terms structures. An easy-ish change.

## 8.0 NOTES

### 8.1 GLOSSARY OF FILE TYPES

FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO
Domain hits file | DHF format (FASTA-like). | Database hits (sequences) with domain classification information. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a discriminating element (e.g. a protein signature, hidden Markov model, simple frequency matrix, Gribskov profile or Hennikoff profile) against a sequence database. | SEQSEARCH (hits retrieved by PSIBLAST). SIGSCAN (hits retrieved by sparse protein signature). LIBSCAN (hits retrieved by various types of HMM and profile). | N.A.
Keywords file | Text | Contains a list of keywords specific to a number of SCOP families and superfamilies used by SEQWORDS to search a sequence database. | N.A. | N.A.

None

## 9.0 DESCRIPTION

Retrieval of domain sequence information from swissprot by mutliple keywords can be a time-consuming process. SEQWORDS parses a file of keywords and the swissprot database and writes a file of sequences whose swissprot entries contains at least one of the keywords. The domain sequence is taken if the keyword appears in the domain record of the feature table, otherwise the full-length sequence is taken.

## 10.0 ALGORITHM

None.

## 11.0 RELATED APPLICATIONS

## See also

Program name | Description
--- | ---
cathparse | Generate DCF file from raw CATH files
domainalign | Generate alignments (DAF file) for nodes in a DCF file
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
matgen3d | Generate a 3D-1D scoring matrix from CCF 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
seqsort | Remove ambiguous classified sequences from DHF files
ssematch | Search a DCF file for secondary structure matches

## 12.0 DIAGNOSTIC ERROR MESSAGES

None.

## 13.0 AUTHORS

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