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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,
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       (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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