maq match

[Lobaria]

Dear all

I am looking for a way to get local read alignments for known genome regions. I have solexa an 454 reads available.

I tried blast searches to find matching reads, maq match to align the reads, and Tablet to look at the local alignment. The problem with this approach is that maq match does not align reads at the endings of the reference. Can anybody recommend a (better) way to do a local assembly that would align reads to the endings?

[epigen]

What do you mean by "maq match does not align reads at the endings of the reference"? If you mean the ends of chromosomes, you usually have a long stretch of Ns there to which od course nothing will map.