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Old 11-09-2010, 03:18 PM   #1
dagarfield
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Location: Heidelberg, Germany

Join Date: Aug 2010
Posts: 39
Default Needed: GAPed alignment tool to save my sequences from the SMART kit

Hi folks,

I'm looking for some recommendations. I've inherited some 454 sequences of cDNA generated using a SMART kit. Perhaps not surprisingly (sigh...see http://seqanswers.com/forums/showthread.php?t=3117) the sequences are contaminated with SMART kit adapters and giant swaths of As or Ts.

BUT, there is hope. Embedded within these sequences are the actual sequences of transcripts that I would like to align to a reference genome (of a closely related species). In effect, the sequences look like this:

BADBADBADBADBAD-GOODGOODGOOD-BADBADBADBADBAD

Can anyone recommend an alignment tool that deals well with gaps such that the good sequence within the bad will align to the reference genome and the BAD portion will be dropped? Out of familiarity, I'm leaning towards using Blastz (or lastz), but there're a whole lot more alignment tools out there than the last time I did this.

Many thanks!

DG
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