[Bioperl-l] DNA sequence assembly for SNP analysis

Chris Fields cjfields at uiuc.edu
Sun Sep 17 10:00:34 EDT 2006


Bioperl has some SNP tools but I'm not sure how up-to-date they are.   
Most of those are accessible via Bio::Cluster, Bio::ClusterIO, and  
Bio::Variation modules.

Chris

On Sep 17, 2006, at 8:06 AM, Fausto Rodríguez Zapata wrote:

> I've found some people that had made po perl scripts for extracting  
> SNPs
> from CAP3 ACE assembly files:
>
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? 
> cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=12584131
>
> http://nar.oxfordjournals.org/cgi/content/full/33/suppl_2/W493
>
>
>
>
> --- Thomas J Keller <kellert at ohsu.edu> wrote:
>
>> Greetings,
>> What are people using for DNA sequence assembly for SNP analysis
>> these days?
>>
>> Thanks,
>> Tom K
>>
>>
>> Thomas J. Keller, Ph.D.
>> Director, MMI Core Facility
>> Oregon Health & Science University
>> 3181 SW Sam Jackson Park Rd.
>> Portland, OR, USA,   97239
>>
>> http://www.ohsu.edu/research/core
>>
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>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






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