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


SEQWORDS(1e)          EMBOSS Manual for Debian          SEQWORDS(1e)

       seqwords - Generates DHF files from keyword search of

       seqwords -keyfile infile -spfile infile -outfile outfile

       seqwords -help

       seqwords 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).

   Input section
       -keyfile infile
           This option specifies the name of keywords file (input).
           This contains a list of keywords specific to a number of
           SCOP or CATH families and superfamilies used by SEQWORDS
           to search a sequence database.

       -spfile infile
           This option specifies the name of the sequence database
           (input) to search.

   Output section
       -outfile outfile
           This option specifies the name of the DHF file (domain
           hits file) (output). A 'domain hits file' contains
           database hits (sequences) with domain classification
           information, in the DHF format (FASTA-like). The hits are
           relatives to a SCOP or CATH family (or other node in the
           structural hierarchies) and are found from a search of a
           sequence database. Files containing hits retrieved by
           PSIBLAST are generated by using SEQSEARCH, hits retrieved
           by a sparse protein signatare by using SIGSCAN or various
           types of HMM and profile by using LIBSCAN. Default value:

       Bugs can be reported to the Debian Bug Tracking system
       (, or directly to the EMBOSS

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

       Debian Med Packaging Team
           Wrote the script used to autogenerate this manual page.

       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                 SEQWORDS(1e)
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