seqsearch(1e) [debian man page]
SEQSEARCH(1e) EMBOSS Manual for Debian SEQSEARCH(1e) NAME
seqsearch - Generate PSI-BLAST hits (DHF file) from a DAF file. SYNOPSIS
seqsearch -mode list -inseqspath dirlist -database string -niter integer -evalue float -maxhits integer -dhfoutdir outdir -logfile outfile seqsearch -help DESCRIPTION
seqsearch 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 -mode list This option specifies the mode of SEQSEARCH operation. SEQSEARCH takes as input a directory of either i. single sequences, ii. set of sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file)). The user has to specify which. Default value: 1 -inseqspath dirlist This option specifies the location of sequences, e.g. DAF files (domain alignment files) (input). SEQSEARCH takes as input a database of either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Default value: ./ -database string Default value: swissprot Required section -niter integer This option specifies the number of PSIBLAST iterations. This option specifies the number of PSIBLAST iterations that are performed in a search. Default value: 1 -evalue float This option specifies the threshold E-value for inclusion in family. This option specifies the threshold E-value for a PSIBLAST hit to be retained. Default value: 0.001 -maxhits integer This option specifies the maximum number of hits. This option specifies the maximum number of PSIBLAST hit that are retained. It should normally be set high so that nothing is discarded. Default value: 1000 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 format. 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: ./ -logfile outfile This option specifies the name of log file for the build. The log file contains messages about any errors arising while SEQSEARCH ran. Default value: seqsearch.log 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
seqsearch 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 SEQSEARCH(1e)
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SEQALIGN(1e) EMBOSS Manual for Debian SEQALIGN(1e) NAME
seqalign - Extend alignments (DAF file) with sequences (DHF file). SYNOPSIS
seqalign -mode list -dhfinpath dirlist -dafinpath dirlist -dhfindir directory -amode list [-forcetype boolean] -dafoutdir outdir -logfile outfile seqalign -help DESCRIPTION
seqalign 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 -mode list This option specifies the mode of SEQALIGN operation. SEQALIGN takes as input a directory of either i. single sequences, ii. set of sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file)). The user has to specify which. Default value: 1 -dhfinpath dirlist This option specifies the location of sequences, e.g. DHF files (domain hits files) (input). SEQALIGN takes as input a database of either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Default value: ./ -dafinpath dirlist This option specifies the location of sequences, e.g. DAF files (domain alignment files) (input). SEQALIGN takes as input a database of either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Default value: ./ -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 -amode list This option specifies which alignment algorithm to use. Default value: 1 Additional section -forcetype boolean This option specifies whether to force minimal domain classification data to be written to the output file in cases where singlet sequences were given as input file and no classification data was available Default value: N Output section -dafoutdir outdir This option specifies the location of DAF files (domain alignment files) (output). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Default value: ./ -logfile outfile This option specifies the name of log file for the build. The log file contains messages about any errors arising while SEQALIGN ran. Default value: seqalign.log 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
seqalign 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. DOMALIGN 0.1.0+20100721 08/11/2010 SEQALIGN(1e)