seqsearch - Generate PSI-BLAST hits (DHF file) from a DAF file.

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DOMSEARCH 0.1.0++20100721                          08/11/2010                                      SEQSEARCH(1e)

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).

       seqsearch - Generate PSI-BLAST hits (DHF file) from a DAF file.

Inputsection-modelist
           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

       -inseqspathdirlist
           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: ./

       -databasestring
           Default value: swissprot

   Requiredsection-niterinteger
           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

       -evaluefloat
           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

       -maxhitsinteger
           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

   Outputsection-dhfoutdiroutdir
           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: ./

       -logfileoutfile
           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

       seqsearch is fully documented via the tfm(1) system.

seqsearch-modelist-inseqspathdirlist-databasestring-niterinteger-evaluefloat-maxhitsinteger-dhfoutdiroutdir-logfileoutfileseqsearch-help