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seqsort.1e.gz

SEQSORT(1e)           EMBOSS Manual for Debian           SEQSORT(1e)



NAME
       seqsort - Remove ambiguous classified sequences from DHF
       files.

SYNOPSIS
       seqsort -dhfindir directory -overlap integer
               -dofamilies toggle -doambiguities toggle
               -dhfoutdir outdir -hitsfile outfile
               -ambigfile outfile

       seqsort -help

DESCRIPTION
       seqsort is a command line program from EMBOSS (“the European
       Molecular Biology Open Software Suite”). It is part of the
       "Protein:3D Structure" command group(s).

OPTIONS
   Input section
       -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. Default value: ./

   Required section
       -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. Default
           value: 10

       -dofamilies toggle
           This option specifies to write a domain families file. If
           this option is set a domain families file is written.
           Default value: N

       -doambiguities toggle
           This option specifies whether to write a domain
           ambiguities file. If this option is set a domain
           ambiguities file is written. Default value: N

   Output section
       -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. Default value: ./

       -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). Default
           value: fam.dhf

       -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). Default
           value: oth.dhf

BUGS
       Bugs can be reported to the Debian Bug Tracking system
       (http://bugs.debian.org/emboss), or directly to the EMBOSS
       developers
       (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO
       seqsort is fully documented via the tfm(1) system.

AUTHOR
       Debian Med Packaging Team
       <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.

COPYRIGHT
       This manual page was autogenerated from an Ajax Control
       Definition of the EMBOSS package. It can be redistributed
       under the same terms as EMBOSS itself.




DOMSEARCH 0.1.0++20100721    08/11/2010                  SEQSORT(1e)
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