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kbws_readme
KEIO Bioinformatics Web Service (https://github.com/gaou/g-language/wiki/kbws)
All rights reserved. Copyright (C) 2010 by OSHITA Kazuki.
This EMBASSY package is free software for non-commercial and education use only (limited due to wsdl2h); you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or any later version expect commercial use.
This is an EMBASSY package for the utilization of bioinformatics web servcie.
All of the tools included in this package are wrapper programs to utilize KBWS SOAP services, which are web APIs to access numerous bioinformatics web services under unified interface with SOAP 1.1.
Detailed documentation about KBWS SOAP services are available at https://github.com/gaou/g-language/wiki/kbws.
EMBOSS (> 6.5.7) - This EMBASSY package requires EMBOSS version 6.5.7 or above.
In the following examples, we assume downloaded EMBOSS filename is EMBOSS-latest.tar.gz (EMBOSS-6.5.7).
- Download and compile EMBOSS source code
% wget ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-latest.tar.gz
(or "curl -O ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-latest.tar.gz")
% tar xzf EMBOSS-latest.tar.gz
% cd EMBOSS-6.5.7
% ./configure
% make
% sudo make install
- Make new directory "embassy" (in EMBOSS-6.5.7/ directory) if it does not exist already
% mkdir embassy
- Go into that directory.
% cd embassy
- Place KBWS file in current directory
% wget http://www.g-language.org/kbws/source/KBWS-1.0.9.tar.gz
(or "curl -O http://www.g-language.org/kbws/source/KBWS-1.0.9.tar.gz")
- Uncompress the KBWS tarball package, and go into the new KBWS directory
% tar xzf KBWS-1.0.9.tar.gz
% cd KBWS-1.0.9
( EMBOSS-6.5.7/embassy/KBWS-1.0.9 )
- Configure and compile
% ./configure (use same options as you used to compile emboss)
% make
% sudo make install
On some systems there may be compatibility problems with different automake, autoconf or libtool versions. If a libtool problem arises you can try deleting the following files:
config.cache
ltmain.sh
ltconfig
libtool
and then type
% aclocal -I m4
% autoconf
% automake -a
and then retry make.
When you are upgrading EMBOSS, please be sure to uninstall old version of EMBOSS and KBWS. If you override them, some older version of files may cause errors.
When EMBOSS is already installed in your system, please install KBWS at the same PATH as existed EMBOSS by '--prefix' option.
If you use "./configure" command with "--prefix" option, please rewrite "emboss_acdroot" and "emboss_data" value in ~ /.embossrc file. Please check "~ /.embossrc" file for further informations.
The database definitions for following commands are available at "KBWS-1.0.9/data/embossrc-template".
The latest version is available at following URL: http://soap.g-language.org/kbws/embossrc
If you want to get list of all tools included in KBWS, you can try the below command.
% wossname -showembassy KBWS
You can view available documentations with "tfm" utility included in EMBOSS.
% tfm kblast # example for "kblast"
Sample files used in this section are available from EMBOSS package. ( EMBOSS-6.4.0/test/data/* )
- kblast (BLAST)
% kblast swissprot:FOXP2_HUMAN -d swissprot -format 8 -eval 1e-100
Search similar sequences in public repositories using BLAST
Output file [foxp2_human.kblast]:
% cat foxp2_human.kblast
query sp|Q8MJ98.3|FOXP2_PONPY 99 457 1 0 240 697 238 695 0.0 2005
query sp|Q5QL03.1|FOXP2_HYLLA 99 457 1 0 240 697 238 695 0.0 2005
query sp|Q8MJ99.1|FOXP2_GORGO 99 457 1 0 240 697 238 695 0.0 2005
query sp|Q8MJA0.1|FOXP2_PANTR 99 457 1 0 240 697 241 698 0.0 2005
query sp|P58463.2|FOXP2_MOUSE 99 457 1 0 240 697 239 696 0.0 2005
query sp|Q8MJ97.1|FOXP2_MACMU 99 457 1 0 240 697 239 696 0.0 2005
query sp|O15409.2|FOXP2_HUMAN 100 458 0 0 240 697 240 697 0.0 2005
query sp|P0CF24.1|FOXP2_RAT 99 456 2 0 240 697 235 692 0.0 2000
query sp|Q4VYS1.1|FOXP2_XENLA 95 450 8 0 240 697 231 688 0.0 1948
query sp|Q5W1J5.1|FOXP1_XENLA 68 373 87 6 240 697 105 560 8e-148 1350
query sp|A4IFD2.1|FOXP1_BOVIN 66 371 89 6 240 697 201 656 4e-146 1335
query sp|Q9H334.1|FOXP1_HUMAN 66 372 89 7 240 697 203 659 2e-144 1321
query sp|Q498D1.1|FOXP1_RAT 65 371 90 7 240 697 237 693 9e-144 1315
query sp|P58462.1|FOXP1_MOUSE 65 372 89 7 240 697 231 687 1e-143 1314
query sp|Q58NQ4.1|FOXP1_CHICK 65 369 92 7 240 697 212 668 1e-143 1313
query sp|Q8IVH2.1|FOXP4_HUMAN 60 332 119 5 240 686 201 650 6e-131 1204
query sp|Q9DBY0.1|FOXP4_MOUSE 60 332 118 17 240 686 207 642 2e-126 1166
query sp|Q4VYR7.1|FOXP4_XENLA 58 336 120 20 241 696 187 622 6e-126 1161
- kcentroidfold (Centroid Fold)
% kcentroidfold
RNA 2D structure prediction from an RNA sequence using CentroidFold
Input (gapped) sequence(s): dna.fasta
Output image file name [kcentroidfold.png]:
Output file [fasta.centroidfold]:
% ls kcentroidfold.png
kcentroidfold.png
% cat fasta.centroidfold
>FASTA
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
((((((((((((((((((((((((((((((((((((((((((((((((....))))))))))))))))))))))))))))))))))))))))))))))))
% wget http://soap.g-language.org/result/13401346.png
- kweblogo (WebLogo)
% kweblogo dna.m-fasta
make the generation of sequence logos using WebLogo
Output file name [kweblogo.png]:
% ls kweblogo.png
kweblogo.png
You can use sample data included in EMBOSS. Please check test/ directory in EMBOSS package.
- gSOAP Toolkit
This EMBASSY package is depended on gSOAP Toolkit to use SOAP transfer, which is included in gsoap/ directory and automatically used during compilation.
Kazuki Oshita < cory@g-language.org >
Institute for Advanced Biosciences, Keio University.
-
G-language Maps
- Institute for Advanced Biosciences
- E-Cell Simulation Environment
- E.coli multi-omics database
- Database of bacterial replication terminus
Kazuharu Arakawa, Ph.D.
G-language Project Leader Associate Professor
Institute for Advanced Biosciences Keio University
997-0017 Japan Tel/Fax: +81-235-29-0800 gaou@sfc.keio.ac.jp