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 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.

DOMALIGN 0.1.0+20100721 					    08/11/2010							   DOMAINALIGN(1e)