Question: Spaln usage after repeatmasking
0
gravatar for abhijit.synl
11 months ago by
abhijit.synl50
United States
abhijit.synl50 wrote:

Hello All,

I was wondering if anyone has used the Spaln program (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488211/ and http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/) 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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1252 users visited in the last hour