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embassy-domsearch - Extra EMBOSS commands to search for protein domains…  more info»

seqsearch.1e.gz

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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