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

NAME

       seqalign - Extend alignments (DAF file) with sequences (DHF file).

SYNOPSIS

       seqalign -mode list -dhfinpath dirlist -dafinpath dirlist -dhfindir directory -amode list [-forcetype boolean] -dafoutdir outdir
		-logfile outfile

       seqalign -help

DESCRIPTION

       seqalign 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
       -mode list
	   This option specifies the mode of SEQALIGN operation. SEQALIGN takes as input a directory of either i. single sequences, ii. set of
	   sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file)). The user has to specify which.
	   Default value: 1

       -dhfinpath dirlist
	   This option specifies the location of sequences, e.g. DHF files (domain hits files) (input). SEQALIGN takes as input a database of
	   either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. A 'domain
	   alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format
	   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: ./

       -dafinpath dirlist
	   This option specifies the location of sequences, e.g. DAF files (domain alignment files) (input). SEQALIGN takes as input a database of
	   either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. A 'domain
	   alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format
	   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: ./

       -dhfindir directory
	   This option specifies the location of DHF files (domain hits files) (input). A 'domain hits file' contains database hits (sequences)
	   with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are
	   found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. Default
	   value: ./

   Required section
       -amode list
	   This option specifies which alignment algorithm to use. Default value: 1

   Additional section
       -forcetype boolean
	   This option specifies whether to force minimal domain classification data to be written to the output file in cases where singlet
	   sequences were given as input file and no classification data was available Default value: N

   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 file is in clustal format 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:
	   ./

       -logfile outfile
	   This option specifies the name of log file for the build. The log file contains messages about any errors arising while SEQALIGN ran.
	   Default value: seqalign.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

       seqalign 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							      SEQALIGN(1e)