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.