| ## SEQSORT 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

Reads DHF files (domain hits files) of database hits (sequences) and removes hits of ambiguous classification

## 2.0 INPUTS & OUTPUTS

SEQSORT reads a directory of DHF files (domain hits files) where each file contains hits to a single SCOP family, compares, processes and collates the hits and writes a directory of DHF files which contain only those hits that could be uniquely assigned to a SCOP family. Optionally, two further files of hits are written: (i) a domain families file, of ALL hits from the input files that could be uniquely assigned to a SCOP family and (ii) a domain ambiguities file, of hits from ALL the input files that are of ambiguous family assignment and are assigned as relatives to a SCOP superfamily or fold instead.
The path for the domain hits files (input and output) and the names of the output files are specified by the user. The file extension of the DHF files are set in the ACD file.

## 3.0 INPUT FILE FORMAT

The format of the domain hits file is described in SEQSEARCH documentation.

## 4.0 OUTPUT FILE FORMAT

The format of the domain hits file is described in SEQSEARCH documentation.
The domain families file and domain ambiguities file also use the DHF format. Whereas normally a DHF file contains hits for a single node from SCOP or CATH, the families and ambiguities files may contain domains from multiple different families (domain families file), or superfamilies or folds (ambiguities file). Domains of the same node (e.g. family) will be grouped together in blocks, i.e. all hits for domain A, then all hits for domain B and so on (see Figure 1).

### Output files for usage example

### File: scop.fam

    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
    NS   27
    XX
    NN   [1]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    AC   Q9YBD5
    XX
    RA   11 START; 105 END;
    XX
    SQ   SEQUENCE    95 AA;  10687 MW;  B8ACF34B CRC32;
         VRKIRSGVVI DHIPPGRAFT MLKALGLLPP RGYRWRIAVV INAESSKLGR KDILKIEGYK
         PRQRDLEVLG IIAPGATFNV IEDYKVVEKV KLKLP
    XX
    NN   [2]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    AC   Q9UX07
    XX
    RA   12 START; 104 END;
    XX
    SQ   SEQUENCE    93 AA;  10312 MW;  12DDDE7C CRC32;
         VSKIRNGTVI DHIPAGRALA VLRILGIRGS EGYRVALVMN VESKKIGRKD IVKIEDRVID
         EKEASLITLI APSATINIIR DYVVTEKRHL EVP
    XX
    NN   [3]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    AC   Q9KP65
    XX
    RA   9 START; 100 END;
    XX

      [Part of this file has been deleted for brevity]

         MMFHKIYIQK HDNVSILFAD IEGFTSLASQ CTAQELVMTL NELFARFDKL AAENHCLRIK
         ILGDCYYCVS GLPEARADHA HCCVEMGVDM IEAISLVREV TGVNVNMRVG IHSGRVHCGV
         LGLRKWQFDV WSNDVTLANH MEAGGRAGRI HITRATLQYL NGDYEVEPGR GGERNAYLKE
         QHIETFLIL
    XX
    NN   [111]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    AC   O30820
    XX
    RA   241 START; 400 END;
    XX
    SQ   SEQUENCE   160 AA;  17506 MW;  B1E1A024 CRC32;
         NIIADKYDEA SVLFADIVGF TERASSTAPA DLVRFLDRLY SAFDELVDQH GLEKIKVSGD
         SYMVVSGVPR PRPDHTQALA DFALDMTNVA AQLKDPRGNP VPLRVGLATG PVVAGVVGSR
         RFFYDVWGDA VNVASRMEST DSVGQIQVPD EVYERLKDDF
    XX
    NN   [112]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    AC   O19179
    XX
    RA   877 START; 1032 END;
    XX
    SQ   SEQUENCE   156 AA;  17212 MW;  675838EA CRC32;
         PEYFEEVTLY FSDIVGFTTI SAMSEPIEVV DLLNDLYTLF DAIIGSHDVY KVETIGDAYM
         VASGLPQRNG QRHAAEIANM ALDILSAVGS FRMRHMPEVP VRIRIGLHSG PCVAGVVGLT
         MPRYCLFGDT VNTASRMEST GLPYRIHVNM STVRIL
    XX
    NN   [113]
    XX
    TY   HIT
    XX
    SC   0.00
    XX
    AC   O02740
    XX
    RA   877 START; 1042 END;
    XX
    SQ   SEQUENCE   166 AA;  18151 MW;  E2BB2824 CRC32;
         PEGFDLVTLY FSDIVGFTTI SAMSEPIEVV DLLNDLYTLF DAIIGSHDVY KVETIGDAYM
         VASGLPKRNG MRHAAEIANM SLDILSSVGT FKMRHMPEVP VRIRIGLHSG PVVAGVVGLT
         MPRYCLFGDT VNTASRMEST GLPYRIHVSH STVTILRTLG EGYEVE
    XX
    //

### File: scop.oth

## 5.0 DATA FILES

None.

## 6.0 USAGE

### 6.1 COMMAND LINE ARGUMENTS

       Standard (Mandatory) qualifiers (* if not always prompted):
      [-dhfindir]          directory  This option specifies the location of DHF
                                      files (domain hits files) (input). A 'domain
                                      hits file' contains database hits
                                      (sequences) with domain classification
                                      information, in the DHF format (FASTA or
                                      EMBL-like). The hits are relatives to a SCOP
                                      or CATH family and are found from a search
                                      of a sequence database. Files containing
                                      hits retrieved by PSIBLAST are generated by
                                      using SEQSEARCH.
       -overlap            integer    This option specifies the number of
                                      overlapping residues required for merging of
                                      two hits. Each family is also processed so
                                      that ovlerapping hits (hits with identical
                                      accesssion number that overlap by at least a
                                      user-defined number of residues) are
                                      replaced by a hit that is produced from
                                      merging the two overlapping hits.
       -dofamilies         toggle     This option specifies to write a domain
                                      families file. If this option is set a
                                      domain families file is written.
       -doambiguities      toggle     This option specifies whether to write a
                                      domain ambiguities file. If this option is
                                      set a domain ambiguities file is written.
      [-dhfoutdir]         outdir     This option specifies the location of DHF
                                      files (domain hits files) (output). A
                                      'domain hits file' contains database hits
                                      (sequences) with domain classification
                                      information, in the DHF format (FASTA or
                                      EMBL-like). The hits are relatives to a SCOP
                                      or CATH family and are found from a search
                                      of a sequence database. Files containing
                                      hits retrieved by PSIBLAST are generated by
                                      using SEQSEARCH.
    *  -hitsfile           outfile    This option specifies the name of domain
                                      families file (output). A 'domain families
                                      file' contains sequence relatives (hits) for
                                      each of a number of different SCOP or CATH
                                      families found from searching a sequence
                                      database, e.g. by using SEQSEARCH
                                      (psiblast). The file contains the collated
                                      search results for the indvidual families;
                                      only those hits of unambiguous family
                                      assignment are included. Hits of ambiguous
                                      family assignment are assigned as relatives
                                      to a SCOP or CATH superfamily or fold
                                      instead and are collated into a 'domain
                                      ambiguities file'. The domain families and
                                      ambiguities files are generated by using
                                      SEQSORT and use the same format as a DHF
                                      file (domain hits file).
    *  -ambigfile          outfile    This option specifies the name of domain
                                      ambiguities file (output). A 'domain
                                      families file' contains sequence relatives
                                      (hits) for each of a number of different
                                      SCOP or CATH families found from searching a
                                      sequence database, e.g. by using SEQSEARCH
                                      (psiblast). The file contains the collated
                                      search results for the indvidual families;
                                      only those hits of unambiguous family
                                      assignment are included. Hits of ambiguous
                                      family assignment are assigned as relatives
                                      to a SCOP or CATH superfamily or fold
                                      instead and are collated into a 'domain
                                      ambiguities file'. The domain families and
                                      ambiguities files are generated by using
                                      SEQSORT and use the same format as a DHF
                                      file (domain hits file).

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

       "-hitsfile" associated qualifiers
       -odirectory         string     Output directory

       "-ambigfile" associated qualifiers
       -odirectory         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
--- | --- | ---
[-dhfindir] (Parameter 1) | This option specifies the location of DHF files (domain hits files) (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. | Directory | ./
-overlap | This option specifies the number of overlapping residues required for merging of two hits. Each family is also processed so that ovlerapping hits (hits with identical accesssion number that overlap by at least a user-defined number of residues) are replaced by a hit that is produced from merging the two overlapping hits. | Any integer value | 10
-dofamilies | This option specifies to write a domain families file. If this option is set a domain families file is written. | Toggle value Yes/No | No
-doambiguities | This option specifies whether to write a domain ambiguities file. If this option is set a domain ambiguities file is written. | Toggle value Yes/No | No
[-dhfoutdir] (Parameter 2) | This option specifies the location of DHF files (domain hits files) (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. | Output directory | ./
-hitsfile | This option specifies the name of domain families file (output). A 'domain families file' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e.g. by using SEQSEARCH (psiblast). The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file). | Output file | fam.dhf
-ambigfile | This option specifies the name of domain ambiguities file (output). A 'domain families file' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e.g. by using SEQSEARCH (psiblast). The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file). | Output file | oth.dhf
Additional (Optional) qualifiers | Allowed values | Default
(none)
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

### 6.2 EXAMPLE SESSION

An example of interactive use of SEQSORT is shown below. Here is a sample session with seqsort

    % seqsort
    Reads multiple files of hits and writes (i) a scop families file and (ii) a
    scop ambiguities file.
    Mode of operation
             1 : Process psiblast hits
             2 : Process swissparse hits (WARNING - untested)
             3 : Merge psiblast and swissparse hits (WARNING - untested)
    Select mode [1]:
    Location of scop hits files (input) [./]: structure
    Extension of scop hits files (input) [.hits]:
    Number of overlapping residues required for merging of two hits [10]: 20
    Name of scop families file (output) [fam.hits]: scop.fam
    Name of ambiguities file (output) [oth.hits]: scop.oth
    Warning: Empty list in embDmxScophitsToHitlist
    Warning: Empty list in embDmxScophitsToHitlist
    Warning: Empty list in embDmxScophitsToHitlist

Go to the output files for this example

All DHF files (of the file extension .dhf specicied in ACD) in directory /test_data were processed by SEQSORT. DHF output files were written to /test_data/seqsort/seqsort_hits. A shared segment of 10 or more identical was required to class two sequences as overlapping. Domain families and ambiguities files called fam.dhf and oth.dhf respectively were written to /test_data/seqsort.

## 7.0 KNOWN BUGS & WARNINGS

None.

## 8.0 NOTES

None.

### 8.1 GLOSSARY OF FILE TYPES

FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO
Domain hits file | DHF format (FASTA-like with domain classification information). | Database hits (sequences) with domain classification information. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. | SEQSEARCH (hits retrieved by PSIBLAST) | N.A.
Domain families & ambiguities file | Contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from PSIBLAST searches of a sequence database. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. | The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file). | N.A.
Domain validation file | Contains sequence relatives (hits) for each of a number of different SCOP or CATH families, superfamilies and folds. The file contains the collated results from PSIBLAST searches of a sequence database for the indvidual families; hits of unambiguous family assignment are listed under their respective family, otherwise a hit is assigned as relatives to a superfamily or fold instead. | The domain validation file is generated by using SEQNR and uses the same format as a DHF file (domain hits file). | N.A.

None

## 9.0 DESCRIPTION

The results of multiple searches of a sequence database using an homology search tool such as blast may contain overlapping or identical hits, especially where the query sequences are related, for instance, belong to different families but the same superfamily. For certain analyses it is desirable to assign a hit with confidence to a unique family, or otherwise assign it as a member of a larger superfamily or fold instead. SEQSORT reads a directory of DHF files (domain hits files) where each file containing hits to a different SCOP family, compares, processes and collates the hits and writes a directory of DHF files which contain only those hits that could be uniquely assigned to a SCOP family. Optionally, two further files are written: (i) a domain families file, of hits (from ALL the input files) that could be uniquely assigned to a SCOP family and (ii) a domain ambiguities file, for hits (from ALL the input files) of ambiguous family assignment which are assigned as relatives to a SCOP superfamily or fold instead.

## 10.0 ALGORITHM

A rough outline of the algorithm follows; a better description will appear in a publication in preparation. Hits from searches for all domain families are collated into a single list and the list sorted according to family name. The hits hits within each family are sorted by accession number, then hits within a family and with identical accession number are sorted by the start position of the hit relative to the full length sequence in swissprot. In each family identical hits (i.e. those with identical accession number and the same start and end points relative to the full-length sequence in swissprot) were removed leaving only a single copy. Each family is also processed so that ovlerapping hits (hits with identical accesssion number that overlap by at least a user-defined number of residues) are replaced by a hit that is produced from merging the two overlapping hits. If two hits have the same accession number and overlap but are from searches for different families, the hits are merged and the merged hit placed into a new list for hits to superfamilies (if the two families belonged to the same superfamily) or for hits to folds (if the two families were in different superfamilies but the same fold). In this way hits that are unique to a particular family are identified, and hits of ambiguous family assignment are assigned as belonging to a superfamily or fold instead.

## 11.0 RELATED APPLICATIONS

## 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
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
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

## 12.0 DIAGNOSTIC ERROR MESSAGES

None.

## 13.0 AUTHORS

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