SYNOPSIS

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

seqsort -help

DESCRIPTION

seqsort

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

AUTHOR

Debian Med Packaging Team <[email protected]>

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.