libscanout(1e) [debian man page]
LIBSCANOUT(1e) EMBOSS Manual for Debian LIBSCANOUT(1e) NAME
libscanout - Reads a DHF file and writes a file of top-scoring Classes, Folds and Superfamilies. SYNOPSIS
libscanout -dhfinfile infile -outfile outfile libscanout -help DESCRIPTION
libscanout 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 -dhfinfile infile This option specifies the location of the DHF file (domain hits file) (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in FASTA or EMBL formats. 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. Required section Output section -outfile outfile This option specifies the location of the summary file (output). The summary file contains lists of domain Classes, Superfamilies and Families rank-ordered on the basis of score (highest-scoring first). 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
libscanout 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. DOMAINATRIX 0.1.0+20100721 08/11/2010 LIBSCANOUT(1e)
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SEQWORDS(1e) EMBOSS Manual for Debian SEQWORDS(1e) NAME
seqwords - Generates DHF files from keyword search of UniProt. SYNOPSIS
seqwords -keyfile infile -spfile infile -outfile outfile seqwords -help DESCRIPTION
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). OPTIONS
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: test.hits 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
seqwords 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 SEQWORDS(1e)