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 outfile

       domainalign -help

DESCRIPTION

       domainalign 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
       -dcfinfile infile
           This option specifies the name of DCF file (domain classification file) (input). A
           'domain classification file' contains classification and other data for domains from
           SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE
           and CATHPARSE. Domain sequence information can be added to the file by using
           DOMAINSEQS.

       -pdbdir directory
           This option specifies the location of domain PDB files (input). A 'domain PDB file'
           contains coordinate data for a single domain from SCOP or CATH, in PDB format. The
           files are generated by using DOMAINER. Default value: ./

   Required section
       -node list
           This option specifies the node for redundancy removal. Redundancy can be removed at
           any specified node in the SCOP or CATH hierarchies. For example by selecting 'Class'
           entries belonging to the same Class will be non-redundant. Default value: 1

       -mode list
           This option specifies the alignment algorithm to use. Default value: 1

       -keepsinglets toggle
           This option specifies whether to write sequences of singlet families to file. If you
           specify this option, the sequence for each singlet family are written to file
           (output). Default value: Y

   Output section
       -dafoutdir outdir
           This option specifies the location of DAF files (domain alignment files) (output). A
           'domain alignment file' contains a sequence alignment of domains belonging to the same
           SCOP or CATH family. The files are in clustal format and are 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: ./

       -singletsoutdir outdir
           This option specifies the location of DHF files (domain hits files) for singlet
           sequences (output). The singlets are written out as a 'domain hits file' - which
           contains database hits (sequences) with domain classification information, in FASTA
           format. Default value: ./

       -superoutdir outdir
           This option specifies the location of structural superimposition files (output). A
           file in PDB format of the structural superimposition is generated for each family if
           the STAMP algorithm is used. Default value: ./

       -logfile outfile
           This option specifies the name of log file (output). The log file contains messages
           about any errors arising while domainalign ran. Default value: domainalign.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

       domainalign 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.