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MAFFT-HOMOLOGS(1)		 Mafft Manual		     MAFFT-HOMOLOGS(1)

NAME
       mafft-homologs -	aligns sequences together with homologues
       automatically collected from SwissProt via NCBI BLAST

SYNOPSIS
       mafft-homologs [options]	input [> output]

DESCRIPTION
       The accuracy of an alignment of a few distantly related sequences is
       considerably improved when being	aligned	together with their close
       homologs. The reason for	the improvement	is probably the	same as	that
       for PSI-BLAST. That is, the positions of	highly conserved residues,
       those with many gaps and	other additional information is	brought	by
       close homologs. According to Katoh et al. (2005), the improvement by
       adding close homologs is	10% or so, which is comparable to the
       improvement by incorporating structural information of a	pair of
       sequences. Mafft-homologs in a mafft server works like this:

	1.  Collect a number (50 by default) of	close homologs (E=1e-10	by
	   default) of the input sequences.

	2.  Align the input sequences and homologs all together	using the
	   L-INS-i strategy.

	3.  Remove the homologs.

OPTIONS
       -a n
	   The number of collected sequences (default: 50).

       -e n
	   Threshold value (default: 1e-10).

       -o xxx
	   Options for mafft (default: " --op 1.53 --ep	0.123 --maxiterate
	   1000	--localpair --reorder").

       -l
	   Locally carries out BLAST searches instead of NCBI BLAST (requires
	   locally installed BLAST and a database).

       -f
	   Outputs collected homologues	also (default: off).

       -w
	   entire sequences are	subjected to BLAST search (default:
	   well-aligned	region only)

REQUIREMENTS
       MAFFT version > 5.58.

       Either of

	   lynx	(when remote BLAST server is used)

	   BLAST and a protein sequence	database (when local BLAST is used)

REFERENCES
       Katoh, Kuma, Toh	and Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT
       version 5: improvement in accuracy of multiple sequence alignment.

SEE ALSO
       mafft(1)

AUTHORS
       Kazutaka	Katoh <katoh_at_bioreg.kyushu-u.ac.jp.>
	   Wrote Mafft.

       Charles Plessy <charles-debian-nospam@plessy.org>
	   Wrote this manpage in DocBook XML for the Debian distribution,
	   using Mafft's homepage as a template.

COPYRIGHT
       Copyright (C) 2002-2007 Kazutaka	Katoh (mafft)
       Copyright (C) 2007 Charles Plessy (this manpage)

       Mafft and its manpage are offered under the following conditions:

       Redistribution and use in source	and binary forms, with or without
       modification, are permitted provided that the following conditions are
       met:

	1.  Redistributions of source code must	retain the above copyright
	   notice, this	list of	conditions and the following disclaimer.

	2.  Redistributions in binary form must	reproduce the above copyright
	   notice, this	list of	conditions and the following disclaimer	in the
	   documentation and/or	other materials	provided with the
	   distribution.

	3.  The	name of	the author may not be used to endorse or promote
	   products derived from this software without specific	prior written
	   permission.

       THIS SOFTWARE IS	PROVIDED BY THE	AUTHOR "AS IS" AND ANY EXPRESS OR
       IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
       WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
       DISCLAIMED. IN NO EVENT SHALL THE AUTHOR	BE LIABLE FOR ANY DIRECT,
       INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
       (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
       SERVICES; LOSS OF USE, DATA, OR PROFITS;	OR BUSINESS INTERRUPTION)
       HOWEVER CAUSED AND ON ANY THEORY	OF LIABILITY, WHETHER IN CONTRACT,
       STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
       IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN	IF ADVISED OF THE
       POSSIBILITY OF SUCH DAMAGE.

mafft-homologs 2.1		  2007-06-09		     MAFFT-HOMOLOGS(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | REQUIREMENTS | REFERENCES | SEE ALSO | AUTHORS | COPYRIGHT

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