Biostar Beta. Not for public use.
Spaln usage after repeatmasking
Entering edit mode
19 months ago
abhijit.synl • 50
United States

Hello All,

I was wondering if anyone has used the Spaln program ( and to map and align cDNA and EST sequences to the genome. I am particularly interested in understanding the Spaln behaviour on soft-masked genomic sequences. Is the behavior similar to BLAT, where the seeding phase avoids the soft-masked regions but the extension phase does not? or does it behave similar to GMAP which does not care for lowercase or uppercase characters. Any information would help a lot.

Thanks Abhijit

Entering edit mode

This should come under "Question" and not "Forum". I have changed the category for now


Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.3.1