kweblogo

Function

Generation of sequence logos using WebLogo

Description

kweblogo is a sequence logo generator utilizing WebLogo. WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.
Sequence Logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens.

kweblogo utilizing WebLogo web service provided by University of California, Berkeley. Original web-service is located at the following URL:

http://weblogo.berkeley.edu/logo.cgi

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. kweblogo is thus an interface of "runWeblogo" 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 kweblogo

% kweblogo
Generation of sequence logos using WebLogo
Input (gapped) sequence(s): test.fasta
Output file name [kweblogo.png]:

% ls kweblogo.png
kweblogo.png

	  

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
[-format]
(Parameter 2)
string [png] Output file format 'png', 'jpeg', 'gif', 'eps', 'pdf' or 'svg' png
[-goutfile]
(Parameter 3)
string [kweblogo.$(format)] Output image file name Any string kweblogo
Additional (Optional) qualifiers
Advanced (Unprompted) qualifiers
(none)

Input file format

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

Output file format

The output from kweblogo is sequence logo image file. This result file is downloaded from KBWS Web server.

Data files

None.

Notes

None.

References

      Schneider, TD., and Stephens, RM.,(1990) Sequence Logos: A New Way to Display
      Consensus Sequences, Nucleic Acids Res, 18, 6097-6100.

      Crooks, GE., et al.,(2004) WebLogo: A sequence logo generator, Genome Research,
      14, 1188-1190.
    

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
edialign Local multiple alignment of sequences
emma Multiple sequence alignment (ClustalW wrapper)
infoalign Display basic information about a multiple sequence alignment
kclustalw Multiple sequence alignment using ClustalW 2
kkalign Multiple sequence alignment using Kalign
kmafft Multiple sequence alignment using MAFFT
kmuscle Multiple sequence alignment using MUSCLE
ktcoffee Multiple sequence alignment using T-COFFEE
plotcon Plot conservation of a sequence alignment
prettyplot Draw a sequence alignment with pretty formatting
seqret Reads and writes (returns) sequences
showalign Display a multiple sequence alignment in pretty format
tranalign Generate an alignment of nucleic coding regions from aligned proteins

Author(s)

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

Hidetoshi Itaya (celery @ g-language.org)
Institute for Advanced Biosciences, Keio University
252-8520 Japan

History

2009 - Written by Kazuki Oshita
Feb 2013 - Function for downloading image file added by Hidetoshi Itaya 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.