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
SEQFRAGGLE(1e) EMBOSS Manual for Debian SEQFRAGGLE(1e) NAME
seqfraggle - Removes fragment sequences from DHF files. SYNOPSIS
seqfraggle -dhfinpath dirlist -thresh integer -dhfoutdir outdir seqfraggle -help DESCRIPTION
seqfraggle 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 -dhfinpath dirlist This option specifies the location of DHF files (domain hits files) or other sequence files (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in FASTA or EMBL formats. 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. Alternatively, SEQFRAGGLE will accept sequence or sequence sets in any of the common formats. Default value: ./ Required section -thresh integer This option specifies the percentage of median length for definition of fragments. SEQFRAGGLE first determines the median length of all the sequences in the input file, then discards any hit sequences which are not within a threshold percentage of the median length. The remaining sequences are written to the output file. Default value: 50 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 FASTA or EMBL formats. 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. Alternatively, SEQFRAGGLE will write output files in any of the common formats. Default value: ./ 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
seqfraggle 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 SEQFRAGGLE(1e)