kclustalw

 

Function

Multiple sequence alignment using ClustalW 2

Description

kclustalw calculates global multiple sequence alignment of DNA and protein sequence utilizing ClustalW 2. ClustalW 2 is a general purpose multiple sequence alignment program for DNA or protein. It calculates the best match for the selected sequence, and lines them up so that identifers, similarities, and differences can be seen.

kclustalw utilizes ClustalW 2 SOAP service provided by EBI (European Bioinformatics Institute). Original web-service is located at the following URL:

http://www.ebi.ac.uk/Tools/clustalw2//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. kclustalw is thus an interface of "runClustalw" 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 kclustalw

% kclustalw
Multiple sequence alignment using ClustalW 2
Input (gapped) sequence(s): swissprot:FOXP2_*
Output file [foxp2_gorgo.aln]: 
Dendrogram (tree file) from clustalw output file [foxp2_gorgo.dnd]: 
Jobid: kbws_7162269
******


 CLUSTAL 2.0.12 Multiple Sequence Alignments


Sequence format is Pearson
Sequence 1: FOXP2_GORGO   713 aa
Sequence 2: FOXP2_HUMAN   715 aa
Sequence 3: FOXP2_HYLLA   713 aa
Sequence 4: FOXP2_MACMU   714 aa
Sequence 5: FOXP2_MOUSE   714 aa
Sequence 6: FOXP2_PANPA   716 aa
Sequence 7: FOXP2_PANTR   716 aa
Sequence 8: FOXP2_PONPY   713 aa
Sequence 9: FOXP2_XENLA   706 aa

 comparing  
paramArg[setSeqNoRange]= off
 comparing 
 Start of Pairwise alignments
Aligning...



Sequences (1:2) Aligned. Score: 99.1585
Sequences (1:3) Aligned. Score: 98.7377
Sequences (1:4) Aligned. Score: 99.439
Sequences (1:5) Aligned. Score: 98.5975
Sequences (1:6) Aligned. Score: 99.439
Sequences (1:7) Aligned. Score: 99.439
Sequences (1:8) Aligned. Score: 98.5975
Sequences (1:9) Aligned. Score: 95.1841
Sequences (2:3) Aligned. Score: 98.5975
Sequences (2:4) Aligned. Score: 99.1597
Sequences (2:5) Aligned. Score: 99.0196
Sequences (2:6) Aligned. Score: 99.1608
Sequences (2:7) Aligned. Score: 99.1608
Sequences (2:8) Aligned. Score: 98.4572
Sequences (2:9) Aligned. Score: 94.6176
Sequences (3:4) Aligned. Score: 99.439
Sequences (3:5) Aligned. Score: 99.2987
Sequences (3:6) Aligned. Score: 98.878
Sequences (3:7) Aligned. Score: 98.878
Sequences (3:8) Aligned. Score: 99.8597
Sequences (3:9) Aligned. Score: 94.6176
Sequences (4:5) Aligned. Score: 98.5994
Sequences (4:6) Aligned. Score: 99.4398
Sequences (4:7) Aligned. Score: 99.4398
Sequences (4:8) Aligned. Score: 99.2987
Sequences (4:9) Aligned. Score: 94.6176
Sequences (5:6) Aligned. Score: 98.7395
Sequences (5:7) Aligned. Score: 98.7395
Sequences (5:8) Aligned. Score: 99.1585
Sequences (5:9) Aligned. Score: 94.7592
Sequences (6:7) Aligned. Score: 100
Sequences (6:8) Aligned. Score: 98.7377
Sequences (6:9) Aligned. Score: 94.6176
Sequences (7:8) Aligned. Score: 98.7377
Sequences (7:9) Aligned. Score: 94.6176
Sequences (8:9) Aligned. Score: 94.4759
Guide tree file created:   [/ebi/extserv/clustalw-work/interactive/2010010801/clustalw2-20100108-0149342273.dnd]

There are 8 groups
Start of Multiple Alignment

Aligning...
Group 1: Sequences:   2      Score:15495
Group 2: Sequences:   3      Score:15449
Group 3: Sequences:   4      Score:15441
Group 4: Sequences:   2      Score:15421
Group 5: Sequences:   3      Score:15417
Group 6: Sequences:   7      Score:15416
Group 7: Sequences:   8      Score:15408
Group 8: Sequences:   9      Score:15019
Alignment Score 153560

CLUSTAL-Alignment file created  [/ebi/extserv/clustalw-work/interactive/2010010801/clustalw2-20100108-0149342273.aln]




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 <*>.kclustalw
[-dndoutfile]
(Parameter 3)
outfile Dendrogram (tree file) from clustalw output file Output file <*>.kclustalw
Additional (Optional) qualifiers
-alignment string method used for pairwise alignment stage Any string full
-output string Alignment output format. Values: 'aln1', 'aln2', 'gcg', 'phylip', 'pir' or 'gde' Any string aln1
-matrix string protein scoring matrix Any string  
-outorder string order of sequences in the alignment Any string aligned
-ktup integer word size Any integer value 0
-window integer window size around best diagonals Any integer value 0
-gapopen integer gap creation penalty Any integer value 0
-gapext float gap extension penalty Any numeric value 0.000
-gapdist integer gap separation penalty Any integer value 0
-endgaps boolean Do not score end gaps Boolean value Yes/No No
-pairgap integer Gap penalty Any integer value 0
-topdiags integer Top diagonals to consider Any integer value 0
-score string score type Any string  
-tossgaps boolean Discard gap regions when calculating tree Boolean value Yes/No No
-kimura boolean Use Kimura's correction Boolean value Yes/No No
-outputtree string Tree format. Values: 'none', 'nj', 'phylip' or 'dist' Any string none
-tree boolean Generate phylogenetic tree Boolean value Yes/No No
-quicktree boolean Perform 'fast' alignment Boolean value Yes/No No
-align boolean Perform alignment Boolean value Yes/No No
-clustering string Tree type. Values: 'nj' or 'upgmp' Any string  
-numiter integer Number of iterations Any integer value 0
-iteration string Iteration type. Values: 'none', 'alignment' or 'tree' Any string none
Advanced (Unprompted) qualifiers
(none)

Input file format

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

Output file format

Output files for usage example

File: foxp2_gorgo.dnd

(
(
(
FOXP2_GORGO:0.00138,
FOXP2_XENLA:0.04678)
:0.00205,
(
(
FOXP2_HYLLA:0.00000,
FOXP2_PONPY:0.00140)
:0.00293,
FOXP2_MOUSE:0.00408)
:0.00359)
:0.00000,
FOXP2_HUMAN:0.00481,
(
FOXP2_MACMU:0.00245,
(
FOXP2_PANPA:0.00000,
FOXP2_PANTR:0.00000)
:0.00315)
:0.00078);



Data files

None.

Notes

None.

References


   Saitou, N., and Nei, M.,(1987) The neighbor-joining method: a new method 
      for reconstructing phylogenetic trees, Mol. Evol. Biol, 4(4), 406-425.

   Higgins, D., et al.,(1994) CLUSTAL W: improving the sensitivity of progressive
      multiple sequence alignment through sequence weighting,position-specific
      gap penalties and weight matrix choice, Nucleic Acids Research, 22, 4673-4680.

   Larkin, M.A., et al.,(2007) ClustalW and ClustalX version 2,
      Bioinformatics 2007, 23(21), 2947-2948.


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
emma Multiple sequence alignment (ClustalW wrapper)

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.

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