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)

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

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)