[Bioc-sig-seq] gapped alignment

[Thomas Girke]

Patrick and Robert,

Thanks for pointing this out. I wasn't aware that such a fast 'SW search' 
option is now available. This will be very useful for many of my own 
applications. 

Allow me to point out here, that I am extremely impressed by the quality and 
utility of the Biostrings package and all the related BioC packages for 
short or long read data analyses. We are using them now on a daily basis for 
all our short read data analyses, and we are extremely happy with their 
performance and functionality.

Thanks for developing all these great resources! 

Thomas 


On Fri, Apr 24, 2009 at 11:50:24AM -0700, Patrick Aboyoun wrote:
> 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 
> >>>>
> >>>>_______________________________________________
> >>>>Bioc-sig-sequencing mailing list
> >>>>Bioc-sig-sequencing at r-project.org
> >>>>https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >>>>
> >>>>        
> >>>_______________________________________________
> >>>Bioc-sig-sequencing mailing list
> >>>Bioc-sig-sequencing at r-project.org
> >>>https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >>>
> >>>      
> >>-- 
> >>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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> >  
> 
>