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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

2. Align the input sequences and homologs all together using the L-INS-i strategy.

3. Remove the homologs.


-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

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.

Either of

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.

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