[Bioperl-l] Affys ReseqChip

Jonathan Epstein Jonathan_Epstein at nih.gov
Thu Apr 12 16:22:40 EDT 2007


This sounds great to me.

Resequencing in general (whether by Affy or by other technology such as Celexa) is likely to become important in the coming few years, and I wonder whether it's worth thinking about a general paradigm for handing this.  But I suggest that you proceed full-speed-ahead, and we can sort this out in the future.

Perhaps one of the experts can advise you whether to use the Bio::UnivAln object, some of the Bio::Assembly objects, or some other approach.

Jonathan


At 12:02 PM 4/11/2007, Marian Thieme wrote:
>Hi,
>
>I am working on a piece of software, which is aimed to analyse the outcome of Affymetrix DNA Resequencing Arrays. (In particular Mitochip V2). The main goal of the software is to take into account for the redundant fragments. The software is able to align the redundant fragments to the entire sequence and in particular to call bases which arent called by the entire sequence and to detect insertions/deletion, depending on the design of the redundant frags.
>
>I would be glad to distribute the software to the bioperl package or otherwise, if anybody is interested I can give the code and/or further develop some features.
>
>Marian

Jonathan Epstein                                Jonathan_Epstein at nih.gov
Head, Unit on Biologic Computation              (301)402-4563
Office of the Scientific Director               Bldg 31, Room 2A47
Nat. Inst. of Child Health & Human Development  31 Center Drive
National Institutes of Health                   Bethesda, MD 20892  


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