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embassy-domalign

Extra EMBOSS commands for protein domain alignment

The DOMALIGN 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 domalign release are allversusall (sequence similarity data from all-versus-all comparison), domainalign (generates alignments (DAF file) for nodes in a DCF file), domainrep (reorders DCF file to identify representative structures) and seqalign (extend alignments (DAF file) with sequences (DHF file)).

Homepage:
Package version:0.1.0+20110714-1
Architecture:s390x
Distribution:Debian
Filename:embassy-domalign_0.1.0+20110714-1_s390x.deb

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

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



NAME
       allversusall - Sequence similarity data from all-versus-all
       comparison.

SYNOPSIS
       allversusall -seqinpath dirlist [-matrix matrixf]
                    [-gapopen float] [-gapextend float]
                    -datoutdir outdir -logfile outfile

       allversusall -help

DESCRIPTION
       allversusall
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/usr/share/man/man1/domainalign.1e.gz

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



NAME
       domainalign - Generate alignments (DAF file) for nodes in a
       DCF file.

SYNOPSIS
       domainalign -dcfinfile infile -pdbdir directory -node list
                   -mode list -keepsinglets toggle -dafoutdir outdir
                   -singletsoutdir outdir -superoutdir outdir
                   -logfile outf
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/usr/share/man/man1/domainrep.1e.gz

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



NAME
       domainrep - Reorder DCF file to identify representative
       structures.

SYNOPSIS
       domainrep -dcfinfile infile -node list -dcfoutfile outfile

       domainrep -help

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

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



NAME
       seqalign - Exten
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/usr/share/doc/embassy-domalign/changelog.Debian.gz

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

  * New upstream version (upstream has ap
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/usr/share/doc/embassy-domalign/copyright

Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: ftp://emboss.open-
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