kkalign

Function

Multiple sequence alignment using Kalign

Description

kkalign calculates multiple sequence alignment utilizing Kalign. Kalign is a fast and accurate multiple sequence alignment algorithm, which handles large sequence.

kkalign utilizes Kalign SOAP service provided by EBI (European Bioinformatics Institute). Original web-service is located at the following URL:

http://www.ebi.ac.uk/Tools/webservices/services/msa/kalign_soap

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. kkalign is thus an interface of "runKalign" 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://www.g-language.org/kbws/ for more information.

Usage


  Here is a sample session with kkalign

% kkalign
Multiple sequence alignment using Kalign
Input (gapped) sequence(s): swissprot:FOXP2_*
Output file [foxp2_gorgo.kkalign]: 

Kalign (2.0) alignment in ClustalW format


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


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


FOXP2_GORGO     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLL-QQQQQQQQQQQQQQQ-QQQQQQQQQQQQ
FOXP2_HUMAN     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ
FOXP2_HYLLA     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLLQQQQQQQQQQQQQQQQ-QQQQQQQQQQQQ
FOXP2_MACMU     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLLQQQQQQQQQQQQQQQQ-QQQQQQQQQQQQ
FOXP2_MOUSE     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ
FOXP2_PANPA     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ
FOXP2_PANTR     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ
FOXP2_PONPY     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLLQQQQQQQQQQQQQQQQ-QQQQQQQQQQQQ
FOXP2_XENLA     LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLL--QQQQQQQQ-QQQQQ-QQQQQQQQQQQQ

	  

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) Required
[-outfile]
(Parameter 2)
outfile Output file name Output file <*>.kkalign
Additional (Optional) qualifiers
-moltype string [auto] Molecular type. 'auto' (auto detection by input sequence), 'N'(nucleotide) or 'P'(protein) Any string auto
-gpo float gap creation penalty Any numeric value 0.000
-gpe float gap extension penalty Any numeric value 0.000
-tgpe float terminal gap penalty Any numeric value 0.000
-bonus float bonus score Any numeric value 0.000
Advanced (Unprompted) qualifiers
(none)

Input file format

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

Output file format

The output from kkalign is ClustalW output format.

Data files

None.

Notes

None.

References

      Lassmann, T., and Erik, S.,(2005) Automatic assessment of alignment quality,
      Nucleic Acids Research, 33(22), 7120-7128.

      Lassmann, T., and Erik, S.,(2005) Kalign - an accurate and fast multiple
      sequence alignment algorithm, BMC Bioinformatics, 6, 298.

      Lassmann, T., and Erik, S.,(2006) Kalign, Kalignvu and Mumsa: web servers
      for multiple sequence alignment, Nucleic Acids Research, 34, W596-W599.
    

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
emma Multiple sequence alignment (ClustalW wrapper)
kclustalw Multiple sequence alignment using ClustalW 2
kmafft Multiple sequence alignment using MAFFT
kmuscle Multiple sequence alignment using MUSCLE
ktcoffee Multiple sequence alignment using T-COFFEE
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
Mar 2013 - Update document by Kazuki Oshita

Target users

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

Comments

None.