Question: Spaln usage after repeatmasking
gravatar for abhijit.synl
11 months ago by
United States
abhijit.synl50 wrote:

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

ADD COMMENTlink modified 11 months ago by lakhujanivijay4.8k • written 11 months ago by abhijit.synl50

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

ADD REPLYlink modified 11 months ago • written 11 months ago by lakhujanivijay4.8k
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