[BioC] Fwd: the diffrent alignment result between pairwiseAlignment() in Biostrings package and EBI-webserver

[Valerie Obenchain]

On 12/28/11 20:36, cao zongfu wrote:
> Anyone can help me?Thanks.
>
> Zongfu

Hi Zongfu,

Martin is out of the office for the holidays. I'm looking at this and 
hope to have an answer for you soon.

Valerie
>
>
> ---------- Forwarded message ----------
> From: cao zongfu<caozongfu at 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 at 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 at 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
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