                            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

   Remove ambiguous classified sequences from DHF files

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: fam.dhf

> Q9YBD5^.^1^95^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^56.10^0.000e+00^9.000e+
00
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNV
IEDYKVVEKVKLKLP
> Q97FS4^.^1^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^43.40^0.000e+00^6.000e+
00
INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEK
IRQKIQLKLP
> Q7MX57^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^73.80^0.000e+00^5.000e+
00
VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIRD
YEVVEKRQVEVP
> P96111^.^1^98^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^43.00^0.000e+00^9.000e+
00
GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNTT
VNIIKNSTVVEKYRIKLP
> Q08462^.^1^167^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^46.20^0.000e+00^4.000e+00
DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQEP
ERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVT
EETSLVL
> Q03101^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^65.80^0.000e+00^4.000e+00
NNACVFFLDIAGFTRFSSIHSPEQVIQVLIKIFNSMDLLCAKHGIEKIKTIGDAYMATCGIFPKCDDIRHNTYKMLGFAM
DVLEFIPKEMSFHLGLQVRVGIHCGPVISGVISGYAKPHFDVWGDTVNVASRMESTGIAGQIHVSDRVY
> Q02153^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^68.90^0.000e+00^4.000e+00
HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPE
PCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEY
TYRCL
> P46197^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^78.50^0.000e+00^7.000e+00
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIA
RMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDE
LGCFQLEL
> P40137^.^1^139^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^48.50^0.000e+00^6.000e+00
VTLLFADIRDFTSLSERLRPEQVVTLLNEYYGRMVEVVFRHGGTLDKFIGDALMVYFGAPIADPAHARRGVQCALDMVQE
LETVNALRSARGEPCLRIGVGVHTGPAVLGNIGSATRRLEYTAIGDTVNLASRIESLTK
> P23466^.^1^154^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^50.80^0.000e+00^1.000e+00
PTGNVAIVFTDIKNSTFLWELFPDAMRAAIKTHNDIMRRQLRIYGGYEVKTEGDAFMVAFPTPTSALVWCLSVQLKLLEA
EWPEEITSIQDGCLITDNSGTKVYLGLSVRMGVHWGCPVPEIDLVTQRMDYLGPVVNKAARVSGVADGGQITLS
> O30820^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^75.40^0.000e+00^6.000e+00
DEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDMT
NVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERL

  File: oth.dhf


  File: 54894.dhf

> Q9YBD5^.^1^95^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^56.10^0.000e+00^9.000e+
00
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNV
IEDYKVVEKVKLKLP
> Q97FS4^.^1^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^43.40^0.000e+00^6.000e+
00
INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEK
IRQKIQLKLP
> Q7MX57^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^73.80^0.000e+00^5.000e+
00
VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIRD
YEVVEKRQVEVP
> P96111^.^1^98^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^.^43.00^0.000e+00^9.000e+
00
GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNTT
VNIIKNSTVVEKYRIKLP

  File: 55074.dhf

> Q08462^.^1^167^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^46.20^0.000e+00^4.000e+00
DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQEP
ERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVT
EETSLVL
> Q03101^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^65.80^0.000e+00^4.000e+00
NNACVFFLDIAGFTRFSSIHSPEQVIQVLIKIFNSMDLLCAKHGIEKIKTIGDAYMATCGIFPKCDDIRHNTYKMLGFAM
DVLEFIPKEMSFHLGLQVRVGIHCGPVISGVISGYAKPHFDVWGDTVNVASRMESTGIAGQIHVSDRVY
> Q02153^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^68.90^0.000e+00^4.000e+00
HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPE
PCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEY
TYRCL
> P46197^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^78.50^0.000e+00^7.000e+00
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIA
RMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDE
LGCFQLEL
> P40137^.^1^139^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^48.50^0.000e+00^6.000e+00
VTLLFADIRDFTSLSERLRPEQVVTLLNEYYGRMVEVVFRHGGTLDKFIGDALMVYFGAPIADPAHARRGVQCALDMVQE
LETVNALRSARGEPCLRIGVGVHTGPAVLGNIGSATRRLEYTAIGDTVNLASRIESLTK
> P23466^.^1^154^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^50.80^0.000e+00^1.000e+00
PTGNVAIVFTDIKNSTFLWELFPDAMRAAIKTHNDIMRRQLRIYGGYEVKTEGDAFMVAFPTPTSALVWCLSVQLKLLEA
EWPEEITSIQDGCLITDNSGTKVYLGLSVRMGVHWGCPVPEIDLVTQRMDYLGPVVNKAARVSGVADGGQITLS
> O30820^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^.^75.40^0.000e+00^6.000e+00
DEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDMT
NVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERL

5.0 DATA FILES

   None.

6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

Remove ambiguous classified sequences from DHF files.
Version: EMBOSS:6.6.0.0

   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    [10] 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)
   -dofamilies         toggle     [N] This option specifies to write a domain
                                  families file. If this option is set a
                                  domain families file is written.
   -doambiguities      toggle     [N] 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    [fam.dhf] 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    [oth.dhf] 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:

   "-dhfindir" associated qualifiers
   -extension1         string     Default file extension

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

   "-hitsfile" associated qualifiers
   -odirectory         string     Output directory

   "-ambigfile" 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


