[Bioc-sig-seq] gapped alignment

[Patrick Aboyoun]

Thomas and Lana,
The pairwiseAlignment() function supports vectorized alignments where 
either a vector of sequences can either be aligned to a single sequence 
or to a vector of sequences where pattern[1] is aligned to subject[1], 
pattern[2] is aligned to subject[2], etc. The looping is then pushed 
down to the C level, which is much faster than looping at the R level.


Patrick


Thomas Girke wrote:
> That's true. The Smith-Waterman alignment algorithm implemented in Biosting's
> pairwiseAlignment() will give even higher sensitivity then BLAST. To use it
> as a search tool, one would simply loop over the database sequences. 
>
> Thomas
>
> On Fri, Apr 24, 2009 at 10:54:48AM -0700, Robert Gentleman wrote:
>   
>> given that it is short, why not use the pairwiseAlignment tool in Biostrings,
>> which would allow you to use gaps +/- quality scores etc?
>>
>>
>>
>> Thomas Girke wrote:
>>     
>>> Dear Lana,
>>>
>>> Using a short-read alignment tool in this case will only work, if 
>>> your virus sequences are extremely similar on the DNA level. If that 
>>> is not the case, then you want to use BLAST, PSI-BLAST, SAM, HMMER or 
>>> any other search tool suited for homolog searching. For detecting 
>>> remote homologs for a coding sequence, you definitely want to perform 
>>> the search on the protein level, because it will be much more sensitive.
>>>
>>> Short-read alignment tools are optimized for aligning very similar
>>> DNA sequences, but not for finding sequences of low similarity. 
>>>
>>> Thomas
>>>
>>>
>>>
>>>
>>> On Fri, Apr 24, 2009 at 07:42:21AM -0700, Lana Schaffer wrote:
>>>       
>>>> Hi,
>>>> I would like advise about how to do gapped alignment
>>>> with output from Solexa sequencing.  We have a new
>>>> virus and would like to know homology to known
>>>> polymerase sequences.  Does someone know if MAQ
>>>> would be a good program for this purpose using
>>>> gapped alignment?  Or would it be best to do
>>>> De Novo alignment and then use Blast?
>>>> Thanks for any advise. 
>>>>
>>>> Lana Schaffer
>>>> Biostatistics/Informatics
>>>> The Scripps Research Institute
>>>> DNA Array Core Facility
>>>> La Jolla, CA 92037
>>>> (858) 784-2263
>>>> (858) 784-2994
>>>> schaffer at scripps.edu 
>>>>
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>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>>
>>>>         
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>>>       
>> -- 
>> Robert Gentleman, PhD
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> PO Box 19024
>> Seattle, Washington 98109-1024
>> 206-667-7700
>> rgentlem at fhcrc.org
>>
>>     
>
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