mafft-homologs man page on DragonFly
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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 © 2002-2007 Kazutaka Katoh (mafft)
Copyright © 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)
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