table of contents
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¶
AUTHORS¶
Kazutaka Katoh <katoh_at_bioreg.kyushu-u.ac.jp.>
- Wrote Mafft.
- 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:
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2007-06-09 | mafft-homologs 2.1 |