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)