seqwords(1e) [debian man page]
SEQWORDS(1e) EMBOSS Manual for Debian SEQWORDS(1e) NAME
seqwords - Generates DHF files from keyword search of UniProt. SYNOPSIS
seqwords -keyfile infile -spfile infile -outfile outfile seqwords -help DESCRIPTION
seqwords 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 -keyfile infile This option specifies the name of keywords file (input). This contains a list of keywords specific to a number of SCOP or CATH families and superfamilies used by SEQWORDS to search a sequence database. -spfile infile This option specifies the name of the sequence database (input) to search. Output section -outfile outfile This option specifies the name of the DHF file (domain hits file) (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA-like). The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH, hits retrieved by a sparse protein signatare by using SIGSCAN or various types of HMM and profile by using LIBSCAN. Default value: test.hits 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
seqwords 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 SEQWORDS(1e)
Check Out this Related Man Page
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)