Does anyone know of any general-purpose semiglobal alignment tools? Something like BLAST for semiglobal alignments instead of local alignments.
A semiglobal alignment is like a global alignment, but penalty-free gaps are allowed at the beginning and end of the alignment. See Wikipedia for a bit more information on semiglobal alignments.
Edit: It has come to my attention that the term "semiglobal alignment" is an ambiguous; it is used to describe several different types of alignment. What I am looking for is a global alignment with no penalty for gaps at the sequence ends.
I want to use ends-free alignment to find all occurrences of a particular sequence in a full lane of Illumina readsI want to mask a short (42 bp) sequence from a lane of paired-end 100 nt Illumina reads. The sequence is expected to occur anywhere within any read with equal probability, including a partial overlap on either end, and if it appears in the middle of a read, it has to be the whole sequence. So I need to do an ends-free alignment of the short sequence against each read independently.