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embassy-domsearch

Extra EMBOSS commands to search for protein domains

Variants:
The DOMSEARCH programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.

Applications in this DOMSEARCH release are seqfraggle (removes fragment sequences from DHF files), seqnr (removes redundancy from DHF files), seqsearch (generates PSI-BLAST hits (DHF file) from a DAF file), seqsort (Remove ambiguous classified sequences from DHF files) and seqwords (Generates DHF files from keyword search of UniProt).

Homepage:
Package version:1:0.1.0+20110714-1
Architecture:s390x
Distribution:Debian
Filename:embassy-domsearch_0.1.0+20110714-1_s390x.deb

/usr/share/man/man1/seqfraggle.1e.gz

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



NAME
       seqfraggle - Removes fragment sequences from DHF files.

SYNOPSIS
       seqfraggle -dhfinpath dirlist -thresh integer
                  -dhfoutdir outdir

       seqfraggle -help

DESCRIPTION
       seqfraggle is a command line program from EMBOSS (“the
       European Molecular Biology Open Software Suite”). 
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/usr/share/man/man1/seqnr.1e.gz

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



NAME
       seqnr - Removes redundancy from DHF files.

SYNOPSIS
       seqnr -dhfinpath dirlist -dosing toggle
             -singletsdir directory -dosets toggle
             -insetsdir directory [-matrix matrixf] -mode list
             -thresh float -threshlow float -threshup float
             [-gapopen float] [-gapextend 
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/usr/share/man/man1/seqsearch.1e.gz

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 i
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/usr/share/man/man1/seqsort.1e.gz

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



NAME
       seqsort - Remove
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/usr/share/man/man1/seqwords.1e.gz

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



NAME
       seqwords - Gener
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/usr/share/doc/embassy-domsearch/changelog.Debian.gz

embassy-domsearch (1:0.1.0+20110714-1) unstable; urgency=low

  * New upstream version
  * debian/co
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/usr/share/doc/embassy-domsearch/changelog.gz

Verion 6.2.0
	In seqsearch, added -t 1 to blastpgp -B command line as the -t
	default has changed an
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/usr/share/doc/embassy-domsearch/copyright

Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: DOMSEARCH
S
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