mafft-homologs - aligns sequences together with homologues
automatically collected from SwissProt via NCBI BLAST
mafft-homologs [options] input [> output]
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
3. Remove the homologs.
The number of collected sequences (default: 50).
Threshold value (default: 1e-10).
Options for mafft (default: " --op 1.53 --ep 0.123 --maxiterate
1000 --localpair --reorder").
Locally carries out BLAST searches instead of NCBI BLAST (requires
locally installed BLAST and a database).
Outputs collected homologues also (default: off).
entire sequences are subjected to BLAST search (default:
well-aligned region only)
MAFFT version > 5.58.
lynx (when remote BLAST server is used)
BLAST and a protein sequence database (when local BLAST is used)
Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT
version 5: improvement in accuracy of multiple sequence alignment.
Kazutaka Katoh <katoh_at_bioreg.kyushu-u.ac.jp.>
Charles Plessy <email@example.com>
Wrote this manpage in DocBook XML for the Debian distribution,
using Mafft’s homepage as a template.
Copyright © 2002-2007 Kazutaka Katoh (mafft)
Copyright © 2007 Charles Plessy (this manpage)
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