Anyone can help me?Thanks.

Zongfu


---------- Forwarded message ----------
From: cao zongfu <caozongfu@gmail.com>
Date: 2011/12/24
Subject: Re: [BioC] the diffrent alignment result between
pairwiseAlignment() in Biostrings package and EBI-webserver
To: Martin Morgan <mtmorgan@fhcrc.org>


Hi, Martin,
     For exmple,

require("Biostrings")
data(BLOSUM62)
x1 =
"QVQLVQSGAEVKKPGSSVKVSCKTSGDTFSTYAISWVRQAPGQGLEWMGGIIPIFGKAHYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYFCARKFHFVSGSPFGMDVWGQGTTVTVSS"
x2 =
"QVQLVESGGDVVQPGGSLRLSCAASGVAFSNYGMHWVRQAPGKGLEWVAVIWYDGSNKYYADSVKGRFTISRDNSKNMLYLQMNSLRAEDTAMYYCARNDDYWGQGTLVTVSS"

alm<- pairwiseAlignment(x1, x2, substitutionMatrix=BLOSUM62, gapOpening=
-10, gapExtension= -0.5,type="global-local")
alm

pattern: [1]
QVQLVQSGAEVKKPGSSVKVSCKTSGDTFSTYAISWVRQAPGQGLEWMGGIIPIFGKAHYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYFCARKFHFVSGSPFGMDVWGQGTTVTVSS
subject: [1]
QVQLVESGGDVVQPGGSLRLSCAASGVAFSNYGMHWVRQAPGKGLEWVAVIWYDGSNKYYADSVKGRFTISRDNSKNMLYLQMNSLRAEDTAMYYCAR
ND----------DYWGQGTLVTVSS

And the result from EBI webserver are as follows
x1      1 QVQLVQSGAEVKKPGSSVKVSCKTSGDTFSTYAISWVRQAPGQGLEWMGG     50
x2      1 QVQLVESGGDVVQPGGSLRLSCAASGVAFSNYGMHWVRQAPGKGLEWVAV     50

x1     51 IIPIFGKAHYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYFCARKF    100
x2     51 IWYDGSNKYYADSVKGRFTISRDNSKNMLYLQMNSLRAEDTAMYYCAR--     98

x1    101 HFVSGSPFGMDVWGQGTTVTVSS    123
x2     99 --------NDDYWGQGTLVTVSS    113


we can find, the position of "ND" are different in the two alignment
result. one is before the gap, and the other after the gap.
Thanks,

Zongfu






2011/12/24 Martin Morgan <mtmorgan@fhcrc.org>
>
> On 12/22/2011 11:54 PM, cao zongfu wrote:
>>
>> Dear Prof., Hi
>>        I have compared the results of pairwise alignment from
>> pairwiseAlignment() in Biostrings package and  the webserver of
>>
http://www.ebi.ac.uk/Tools/services/web/toolform.ebi?tool=emboss_needle&context=protein
,
>> I found the results are different.
>>
>> EBI-web parameters are as follows,
>> #matrix=BLOSUM62
>> #GAP OPEN=10
>> #GAP EXTEND=0.5
>> #OUTPUT FORMAT="PAIR"
>> #END GAP PENALTY=FALSE
>> #END GAP OPEN=10
>> #END GAP EXTEND=0.5
>> and the parameters in pairwiseAlignment() are as follows,
>> alm<- pairwiseAlignment(x1, x2, substitutionMatrix=BLOSUM62, gapOpening=
>> -10, gapExtension= -0.5,type="global-local")
>>
>> I have tried to set the type="global", they all wored well, but the
>> alignment result is still different.I want to know how to set other
>> parameters in order to get the identical alignment result as EBI
webserver?
>
>
> can you provide a more explicit example, with sequences x1 and x2 as well
as the output from the two programs? Martin
>
>>
>> Thanks,
>>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793




--

Zongfu Cao

BeiGene(Beijing) Co.,Ltd
No.30 Science Park Road
Zhong-Guan-Cun Life Science Park
Changping District, Beijing P.R.China
Postal Code: 102206




-- 

Zongfu Cao

*BeiGene(Beijing) Co.,Ltd*
No.30 Science Park Road
Zhong-Guan-Cun Life Science Park
Changping District, Beijing P.R.China
Postal Code: 102206

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