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Spaln usage after repeatmasking
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19 months ago
abhijit.synl • 50
United States

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

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

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