'\" t .\" Title: SEQSORT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMSEARCH 0.1.0++20100721 .\" Language: English .\" .TH "SEQSORT" "1e" "08/11/2010" "DOMSEARCH 0.1.0++20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqsort \- Remove ambiguous classified sequences from DHF files\&. .SH "SYNOPSIS" .HP \w'\fBseqsort\fR\ 'u \fBseqsort\fR \fB\-dhfindir\ \fR\fB\fIdirectory\fR\fR \fB\-overlap\ \fR\fB\fIinteger\fR\fR \fB\-dofamilies\ \fR\fB\fItoggle\fR\fR \fB\-doambiguities\ \fR\fB\fItoggle\fR\fR \fB\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-hitsfile\ \fR\fB\fIoutfile\fR\fR \fB\-ambigfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBseqsort\fR\ 'u \fBseqsort\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqsort\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dhfindir\fR \fIdirectory\fR .RS 4 This option specifies the location of DHF files (domain hits files) (input)\&. A \*(Aqdomain hits file\*(Aq 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: \&./ .RE .SS "Required section" .PP \fB\-overlap\fR \fIinteger\fR .RS 4 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 .RE .PP \fB\-dofamilies\fR \fItoggle\fR .RS 4 This option specifies to write a domain families file\&. If this option is set a domain families file is written\&. Default value: N .RE .PP \fB\-doambiguities\fR \fItoggle\fR .RS 4 This option specifies whether to write a domain ambiguities file\&. If this option is set a domain ambiguities file is written\&. Default value: N .RE .SS "Output section" .PP \fB\-dhfoutdir\fR \fIoutdir\fR .RS 4 This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq 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: \&./ .RE .PP \fB\-hitsfile\fR \fIoutfile\fR .RS 4 This option specifies the name of domain families file (output)\&. A \*(Aqdomain families file\*(Aq 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 \*(Aqdomain ambiguities file\*(Aq\&. 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 .RE .PP \fB\-ambigfile\fR \fIoutfile\fR .RS 4 This option specifies the name of domain ambiguities file (output)\&. A \*(Aqdomain families file\*(Aq 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 \*(Aqdomain ambiguities file\*(Aq\&. 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 .RE .SH "BUGS" .PP 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)\&. .SH "SEE ALSO" .PP seqsort is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP 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\&. .sp