[Bioc-sig-seq] gapped alignment

[Robert Gentleman]

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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>>
> 
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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