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Old 11-16-2010, 01:20 AM   #2
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Location: WashU

Join Date: Aug 2010
Posts: 117

It seems like the next-gen, fast, short read aligners are generally focused on aligning entire reads and do not do substring alignments. You may be stuck using an old school aligner. BLAST will certainly do what you are describing. BLAT or Exonerate would also probably be fine. If you are aligning cDNAs to a genome you could also use splice aware aligners such as Spidey or Splign. Of course all of these options are way, way slower. Maybe someone else will suggest other options.
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