kmafft

 

Function

Multiple sequence alignment using MAFFT

Description

kmafft calculates the multiple sequence alignment utilizing MAFFT. MAFFT has various multiple sequence alignment. They are classified to three types, the progressive method, the iterative refinement method with the WSP score, and the iterative refinement method using both the WSP and consistency score.

kmafft utilizes MAFFT version 6 Online version provided by Kyushu Univ. Original web-service is located at the following URL:

http://align.bmr.kyushu-u.ac.jp/mafft/online/server//cgi-bin/emboss/help

This tools is a subset of Keio Bioinformatics Web Service (KBWS) package, which contains interfaces to bioinformatics web services through a proxy server at Keio University. kmafft is thus an interface of "runMafft" method included in KBWS SOAP service. This method can be alternatively accessed directly from programming languages as SOAP web service. Please refer to the KBWS online documentations http://soap.g-language.org/kbws/ for more information.

Usage


   Here is a sample session with kmafft

% kmafft
Multiple sequence alignment using MAFFT
Input (gapped) sequence(s): swissprot:FOXP2_*
Output file [foxp2_gorgo.kmafft]: 
Jobid: kbws_3935052
**

CLUSTAL format alignment by MAFFT (v6.713b)


FOXP2_GORGO     MMQESATETISNSSMNQNGMSTLSSQLDAGSRDGRSSGDTSSEVSTVELLHLQQQQALQA
FOXP2_MACMU     MMQESATETISNSSMNQNGMSTLSSQLDAGSRDGRSSGDTSSEVSTVELLHLQQQQALQA
FOXP2_PANPA     MMQESATETISNSSMNQNGMSTLSSQLDAGSRDGRSSGDTSSEVSTVELLHLQQQQALQA
FOXP2_PANTR     MMQESATETISNSSMNQNGMSTLSSQLDAGSRDGRSSGDTSSEVSTVELLHLQQQQALQA
FOXP2_HYLLA     MMQESATETISNSSMNQNGMSTLSSQLDAGSRDGRSSGDTSSEVSTVELLHLQQQQALQA
FOXP2_PONPY     MMQESVTETISNSSMNQNGMSTLSSQLDAGSRDGRSSGDTSSEVSTVELLHLQQQQALQA
FOXP2_MOUSE     MMQESATETISNSSMNQNGMSTLSSQLDAGSRDGRSSGDTSSEVSTVELLHLQQQQALQA
FOXP2_HUMAN     MMQESATETISNSSMNQNGMSTLSSQLDAGSRDGRSSGDTSSEVSTVELLHLQQQQALQA
FOXP2_XENLA     MMQESATETISNSSMNQNGMSTLSSQLDAGSRDGRSSSDTSSEVSTVELLHLQQQQALQA
                *****.*******************************.**********************

FOXP2_GORGO     ARQLLLQQQTSGLKSPKSSDKQRPLQVPVSVAMMTPQVITPQQMQQILQQQVLSPQQLQA
FOXP2_MACMU     ARQLLLQQQTSGLKSPKSSDKQRPLQVPVSVAMMTPQVITPQQMQQILQQQVLSPQQLQA
FOXP2_PANPA     ARQLLLQQQTSGLKSPKSSDKQRPLQVPVSVAMMTPQVITPQQMQQILQQQVLSPQQLQA
FOXP2_PANTR     ARQLLLQQQTSGLKSPKSSDKQRPLQVPVSVAMMTPQVITPQQMQQILQQQVLSPQQLQA
FOXP2_HYLLA     ARQLLLQQQTSGLKSPKSSDKQRPLQVPVSVAMMTPQVITPQQMQQILQQQVLSPQQLQA
FOXP2_PONPY     ARQLLLQQQTSGLKSPKSSDKQRPLQVPVSVAMMTPQVITPQQMQQILQQQVLSPQQLQA
FOXP2_MOUSE     ARQLLLQQQTSGLKSPKSSEKQRPLQVPVSVAMMTPQVITPQQMQQILQQQVLSPQQLQA
FOXP2_HUMAN     ARQLLLQQQTSGLKSPKSSDKQRPLQVPVSVAMMTPQVITPQQMQQILQQQVLSPQQLQA
FOXP2_XENLA     ARQLLLQQQTSGLKSPKNNEKQRPLQVPVSMAMMTPQVITPQQMQQILQQQVLSPQQLQA
                *****************..:**********:*****************************

FOXP2_GORGO     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLL---QQQQQQQQQQQQQQQQQQQQQQQQQQ
FOXP2_MACMU     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLL--QQQQQQQQQQQQQQQQQQQQQQQQQQQ
FOXP2_PANPA     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ
FOXP2_PANTR     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ
FOXP2_HYLLA     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLL--QQQQQQQQQQQQQQQQQQQQQQQQQQQ
FOXP2_PONPY     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLL--QQQQQQQQQQQQQQQQQQQQQQQQQQQ
FOXP2_MOUSE     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLL-QQQQQQQQQQQQQQQQQQQQQQQQQQQQ
FOXP2_HUMAN     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLL-QQQQQQQQQQQQQQQQQQQQQQQQQQQQ

Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-seqall]
(Parameter 1)		 seqall (Gapped) sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) 2
[-outfile]
(Parameter 2)		 outfile Output file name Output file <*>.kmafft
Additional (Optional) qualifiers
-strategy string strategy to calculate Any string auto
-outorder string output order Any string aligned
-op float gap opening penalty (1.0 - 3.0) Any numeric value 1.53
-ep float offset value (0.0 - 1.0) Any numeric value 0.0
-scorematrix string scoring matrix Any string  
-homologs boolean collects homologs (only protein) Boolean value Yes/No No
-showhomologs boolean show homologs (if any) Boolean value Yes/No No
-numhomologs integer number of homologs Any integer value 50
-threshold float threshold of homologs Any numeric value 1e-10
-referenceseq string sorry. this option is not ready Any string  
-harrplot string sorry. this option is not ready. Any string  
Advanced (Unprompted) qualifiers
(none)

Input file format

kmafft can use any genome sequence data that seqret can read.

Output file format

The output from kmafft is general MAFFT output format (CLUSTAL format alignment).

Data files

None.

Notes

None.

References


   Katoh, K.,(2009) Multiple Alignment of DNA Sequences with MAFFT,
      Methods in Molecular Biology, 537, 39-64.

   Katoh, K., and Toh, H.,(2008) Recent developments in the MAFFT multiple
      sequence alignment program, Briefings in Bioinformatics, 9, 286-298.

   Katoh, K., et al.,(2005) MAFFT version 5: improvement in accuracy of multiple
      sequence alignment, Nucleic Acids Res, 33, 511-518.

   Katoh, K., et al.,(2002) MAFFT: a novel method for rapid multiple sequence
      alignment based on fast, Nucleic Acids Res, 30, 3059-3066.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
seqret Reads and writes (returns) sequences

Author(s)

Kazuki Oshita (cory @ g-language.org) Institute for Advanced Biosciences, Keio University 252-8520 Japan

History

2009 - Written by Kazuki Oshita

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments