[BioC] difference results by needle program and pairwiseAlignment

[Hervé Pagès]

On 12/06/2012 02:15 PM, Wang Peter wrote:
> dear Herve：
> Thank you for your help
>
> my needle setting is default
>>> # Matrix: EBLOSUM62
>>> # Gap_penalty: 10.0
>>> # Extend_penalty: 0.5
>>
> and the score is 6
>
> how can i set the pairwiseAlignment
> Gap_penalty: ?
> Extend_penalty: ?
>

The answer is in my previous email. We know you are fast but managing
to read and understand my previous email + the man page for
writePairwiseAlignments (as suggested) + do a little bit of your own
experimentation with different settings (type="global",
type="global-local", etc...) in order to understand how they affect
the output will probably take you more than 9 minutes.

Cheers,
H.

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

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