[Genome] optimal settings for aligning medium length oligos

[Mark Cowley]

Hello, and thanks for providing such a fantastic resource.

I am using stand alone BLAT, and aligning 50mers and 65mers to the mouse
and human genomes.

Can you please tell me the optimal settings for aligning:
65mers to the genome?
50mers to the genome?

thank you

Mark

Mark Cowley
PhD candidate

Systems Biology Laboratory 2 (room 263)
School of Biotechnology and Biomolecular Sciences
University of New South Wales
NSW, 2052, Australia

email:   mark.cowley at student.unsw.edu.au
web:     http://www.babs.unsw.edu.au/