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)