[BioRuby] Help using EMBOSS in Bioruby...
Toshiaki Katayama
ktym at hgc.jp
Wed Jan 9 02:42:12 UTC 2008
Sharvari,
Sorry, I missed your previous mails.
On 2008/01/03, at 4:53, Sharvari Gujja wrote:
> Hi,
>
> I was wondering how to use water and needle emboss tools in Bioruby. I am aware that the class Bio::EMBOSS exists with methods:
>
> *entret*(arg) src <http://bioruby-doc.org/rdoc/classes/Bio/EMBOSS.src/M000989.html>
> *new*(cmd_line) src <http://bioruby-doc.org/rdoc/classes/Bio/EMBOSS.src/M000990.html>
>
> *seqret*(arg) src <http://bioruby-doc.org/rdoc/classes/Bio/EMBOSS.src/M000988.html>
>
>
> *exec*() src <http://bioruby-doc.org/rdoc/classes/Bio/EMBOSS.src/M000991.html>
>
> I would like to know how to use water and needle tools.I really appreciate your help.
>
> Thanks
> Sharvari
On 2008/01/08, at 5:47, Sharvari Gujja wrote:
> Hello Mr.Toshiaki,
>
> First off, I'd like to thank you for all your help.
>
> I have just one more question for you. I am trying to see how to use Smith-Waterman / Needleman Wunch alignment in Bioruby.
> I really appreciate any input from you.
>
> Thanks
> Sharvari
There are several ways to do it. Simplest version would be
result = `water -asequence 'swissprot:slpi_human' -bsequence 'swissprot:slpi_mouse' -stdout -auto`
and usage of the Bio::EMBOSS class is well documented in the source code.
http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioruby//lib/bio/appl/emboss.rb?rev=1.8&cvsroot=bioruby
bioruby> puts Bio::EMBOSS.new("water -asequence 'swissprot:slpi_human' -bsequence 'swissprot:slpi_mouse'").exec
########################################
# Program: water
# Rundate: Wed 9 Jan 2008 11:22:59
# Commandline: water
# -asequence swissprot:slpi_human
# -bsequence swissprot:slpi_mouse
# -stdout
# -auto
# Align_format: srspair
# Report_file: stdout
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: SLPI_HUMAN
# 2: SLPI_MOUSE
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 132
# Identity: 79/132 (59.8%)
# Similarity: 96/132 (72.7%)
# Gaps: 3/132 ( 2.3%)
# Score: 464.5
#
#
#=======================================
SLPI_HUMAN 1 MKSSGLFPFLVLLALGTLAPWAVEGSGK--SFKAGVCPPKKSAQCLRYKK 48
|||.||.||.||||||.||||.||| || :.|.|.||.||.||||:.:|
SLPI_MOUSE 1 MKSCGLLPFTVLLALGILAPWTVEG-GKNDAIKIGACPAKKPAQCLKLEK 49
SLPI_HUMAN 49 PECQSDWQCPGKKRCCPDTCGIKCLDPVDTPNPTRRKPGKCPVTYGQCLM 98
|:|::||:||||:|||.|.||.||::||....|..||||:|..|..:|:|
SLPI_MOUSE 50 PQCRTDWECPGKQRCCQDACGSKCVNPVPIRKPVWRKPGRCVKTQARCMM 99
SLPI_HUMAN 99 LNPPNFCEMDGQCKRDLKCCMGMCGKSCVSPV 130
|||||.|:.||||....|||.|:|||.|:.|:
SLPI_MOUSE 100 LNPPNVCQRDGQCDGKYKCCEGICGKVCLPPM 131
#---------------------------------------
#---------------------------------------
==> nil
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