| seqwords

## Function

Generates DHF files (domain hits files) of database hits (sequences) for nodes in a DCF file (domain classification file) by keyword search of UniProt

## Description

**************** EDIT HERE ****************

## Algorithm

**************** EDIT HERE ****************

## Usage

Here is a sample session with seqwords

    % seqwords
    Generates DHF files (domain hits files) of database hits (sequences) for
    nodes in a DCF file (domain classification file) by keyword search of
    UniProt.
    Name of keywords file (input): seqwords.terms
    Name of sequence database (input): seqwords.seq
    Name of DHF file (domain hits file) (output) [test.hits]: seqwords.dhf

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

## Command line arguments

       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    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 standard output
       -filter             boolean    Read standard input, write 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. 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 deaths

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-keyfile] (Parameter 1) | 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) | This option specifies the name of the sequence database (input) to search. | Input file | Required
[-outfile] (Parameter 3) | 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 | Allowed values | Default
(none)
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

seqwords reads any normal sequence USAs.

### 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
    //

## Output file format

seqwords outputs a graph to the specified graphics device. outputs a report format file. The default format is ...

### 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

## Data files

**************** EDIT HERE ****************

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
contactcount | Counts specific versus non-specific contacts in a directory of cleaned protein chain contact files
contacts | Reads CCF files (clean coordinate files) and writes CON files (contact files) of intra-chain residue-residue contact data
domainalign | Generates DAF files (domain alignment files) of structure-based sequence alignments for nodes in a DCF file (domain classification file)
domainrep | Reorder DCF file (domain classification file) so that the representative structure of each user-specified node is given first
domainreso | Removes low resolution domains from a DCF file (domain classification file)
interface | Reads CCF files (clean coordinate files) and writes CON files (contact files) of inter-chain residue-residue contact data
libgen | Generates various types of discriminating elements for each alignment in a directory
psiphi | Calculates phi and psi torsion angles from cleaned EMBOSS-style protein co-ordinate file
rocon | Reads a DHF file (domain hits file) of hits (sequences of unknown structural classification) and a DHF file of validation sequences (known classification) and writes a 'hits file' for the hits, which are classified and rank-ordered on the basis of score
rocplot | Provides interpretation and graphical display of the performance of discriminating elements (e.g. profiles for protein families). rocplot reads file(s) of hits from discriminator-database search(es), performs ROC analysis on the hits, and writes graphs illustrating the diagnostic performance of the discriminating elements
seqalign | Reads a DAF file (domain alignment file) and a DHF file (domain hits file) and writes a DAF file extended with the hits
seqfraggle | Removes fragments from DHF files (domain hits files) or other files of sequences
seqsearch | Generate database hits (sequences) for nodes in a DCF file (domain classification file) by using PSI-BLAST
seqsort | Reads DHF files (domain hits files) of database hits (sequences) and removes hits of ambiguous classification
siggen | Generates a sparse protein signature from an alignment and residue contact data
sigscan | Generates a DHF file (domain hits file) of hits (sequences) from scanning a signature against a sequence database

## Author(s)

Jon Ison (jison © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

## History

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.