This is the command mafft-homologs that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
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.
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
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.
Use mafft-homologs online using onworks.net services