seqsort - Remove ambiguous classified sequences from DHF files.

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

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).

       seqsort - Remove ambiguous classified sequences from DHF files.

Inputsection-dhfindirdirectory
           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: ./

   Requiredsection-overlapinteger
           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

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

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

   Outputsection-dhfoutdiroutdir
           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: ./

       -hitsfileoutfile
           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

       -ambigfileoutfile
           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

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

seqsort-dhfindirdirectory-overlapinteger-dofamiliestoggle-doambiguitiestoggle-dhfoutdiroutdir-hitsfileoutfile-ambigfileoutfileseqsort-help