[BioRuby] Calculation of Conserved residues.
Yonatan Gross
gross_yonatan at yahoo.com
Sat Apr 7 23:31:39 UTC 2007
Hi all, first post to this group. I hope this question is legit.
I am trying to quantify the alignment of few genes.
with mac vector I am able to get a "conserved Identities" value i
can use , but I need to manually run the clustalw procedure.
I want to write a ruby script to do the same.
any suggestions ?
I have the following:
#!/usr/bin/env ruby
require 'rubygems'
require 'bio'
#-----------------------------------------------------------------------
--
arabidopsis = <<END
>gi|9843639|emb|CAC03598.1| Rieske FeS protein [Arabidopsis thaliana]
MASSSLSPATQLGSSRSALMAMSSGLFVKPTKMNHQMVRKEKIGLRIACQASSIPADRVPDMEKRKTLNL
LLLGALSLPTGYMLVPYATFFVPPGTGGGGGGTPAKDALGNDVVAAEWLKTHGPGDRTLTQGLKGDPTYL
VVENDKTLATYGINAVCTHLGCVVPWNKAENKFLCPCHGSQYNAQGRVVRGPAPLSLALAHADIDEAGKV
LFVPWVETDFRTGDAPWWS
END
tobacco = <<END
>gi|19995|emb|CAA46808.1| Rieske FeS [Nicotiana tabacum]
MASSTLSPVTQLCSSKSGLSSVSQCLLVKPMKINSHGLGKDKRMKVKCMATSIPADDRVPDMEKRNLMNL
LLLGALSLPTAGMLVPYGTFFVPPGSGGGSGGTPAKDALGNDVIASEWLKTHPPGNRTLTQGLKGDPTYL
VVENDGTLATYGINAVCTHLGCVVPFNAAENKFICPCHGSQYNNQGRVVRGPAPLSLALAHADIDDGKVV
FVPWVETDFRTGEDPWWA
END
spinach = <<END
>gi|226151|prf||1412276A rieske FeS precursor protein [spinach]
MIISIFNQLHLTENSSLMASFTLSSATPSQLCSSKNGMFAPSLALAKAGRVNVLISKERIRGMKLTCQAT
SIPADNVPDMQKRETLNLLLLGALSLPTGYMLLPYASFFVPPGGGAGTGGTIAKDALGNDVIAAEWLKTH
APGDRTLTQGLKGDPTYLVVESDKTLATFGINAVCTHLGCVVPFNAAENKFICPCHGSQYNNQGRVVRGP
APLSLALAHCDVDDGKVVFVPWTETDFRTGEAPWWSA
END
rice = <<END
>gi|115472727|ref|NP_001059962.1| Os07g0556200 [Oryza sativa
(japonica cultivar-group)]
MASTALSTASNPTQLCRSRASLGKPVKGLGFGRERVPRTATTITCQAASSIPADRVPDMGKRQLMNLLLL
GAISLPTVGMLVPYGAFFIPAGSGNAGGGQVAKDKLGNDVLAEEWLKTHGPNDRTLTQGLKGDPTYLVVE
ADKTLATYGINAVCTHLGCVVPWNAAENKFICPCHGSQYNNQGRVVRGPAPLSLALVHADVDDGKVLFVP
WVETDFRTGDNPWWA
END
potato = <<END
>gi|37222949|gb|AAQ90151.1| putative Rieske Fe-S protein precursor
[Solanum tuberosum]
MASSTLSHVTPSQLCSSKSGVSSVSQALLVKPMKINGHGMGKDKRMKAKCMAASIPADDRVPDMEKRNLM
NLLLLGALALPTGGMLVPYATFFAPPGSGGGSSGTIAKDANGNDVVVTEWLKTHSPGTRTLTQGLKGDPT
YLVVENDGTLATYGINAVCTHLGCVVPWNTAENKFICPCHGSQYNNQGKVVRGPAPLSLALAHADIDDGK
VVFVPWVETDFRTGDSPWWA
END
seqs = []
seqs << Bio::Sequence::AA.new(arabidopsis)
seqs << Bio::Sequence::AA.new(tobacco)
seqs << Bio::Sequence::AA.new(spinach)
seqs << Bio::Sequence::AA.new(rice)
seqs << Bio::Sequence::AA.new(potato)
factory = Bio::ClustalW.new
report = factory.query_align(seqs)
puts report.alignment.match_line
#-----------------------------------------------------------------------
--
thanks ahead.
Yonatan Gross.
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