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embassy-domainatrix

Extra EMBOSS commands to handle domain classification file

Variants:
The DOMAINATRIX 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 the current domainatrix release are cathparse (generates DCF file from raw CATH files), domainnr (removes redundant domains from a DCF file), domainreso (removes low resolution domains from a DCF file), domainseqs (adds sequence records to a DCF file), domainsse (adds secondary structure records to a DCF file), scopparse (generates DCF file from raw SCOP files) and ssematch (searches a DCF file for secondary structure matches).

Homepage:
Package version:0.1.0+20110714-1
Architecture:s390x
Distribution:Debian
Filename:embassy-domainatrix_0.1.0+20110714-1_s390x.deb

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

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



NAME
       cathparse - Generates DCF file from raw CATH files.

SYNOPSIS
       cathparse -listfile infile -domfile infile -namesfile infile
                 -outfile outfile -logfile outfile

       cathparse -help

DESCRIPTION
       cathparse is a command line program from EMBOSS (“the
       European Molecular Biology O
more»

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

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



NAME
       domainnr - Removes redundant domains from a DCF file.

SYNOPSIS
       domainnr -dcfinfile infile [-datafile matrixf] -retain toggle
                -node list -mode list -threshold float
                -threshlow float -threshup float [-gapopen float]
                [-gapextend float] -dcfoutfile outfile
       
more»

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

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



NAME
       domainreso - Remove low resolution domains from a DCF file.

SYNOPSIS
       domainreso -cpdbpath dirlist -dcfinfile infile
                  -threshold float -dcfoutfile outfile

       domainreso -help

DESCRIPTION
       domainreso is a command line program from EMBOSS (“the
       European Molecular Biology O
more»

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

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



NAME
       domainseqs - Add
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/usr/share/man/man1/domainsse.1e.gz

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



NAME
       domainsse - Add 
more»

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

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



NAME
       libscan - Diagno
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/usr/share/man/man1/libscanout.1e.gz

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



NAME
       libscanout - Rea
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/usr/share/man/man1/scopparse.1e.gz

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



NAME
       scopparse - Gene
more»

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