Align short oligonucleotide sequences to a longer sequence
Posted: Thu Nov 08, 2012 12:06 pmFor aligning small DNA fragments to a longer sequence please make sure to change the alignment preferences in CodonCode Aligner. Use the "End to end alignments" setting and change the following alignment parameters to be smaller than the DNA fragments that you want to align:
- - Min. overlap length
- Min. score
- Word length