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Can I send many different short DNA sequences on to any genome of interest and get sequences that do not match the genome under study?

I am a basic programmer looking for a small code in java (preferably) or R such that I can send different short length DNA sequences (10 to 100 base) on to any genome in NCBI website and get sequences that are not similar or complementary to the respective genome under study. I used BLAST but most of them are being aligned by this software by force (75% similarity). Your help is much appreciated, Thank you in advance.

alignment gene blast genome
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updated by Ram Ram • written by nsknadendla • nsknadendla

Get the blast results and then filter out weak hits you don't want.

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written by lh3 lh3

I think that it is a similar problem to mapping reads to contigs. This can be done with bbmap. You coudl give it a look, but it is not a web tool.

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written by dago dago

Dago thank you for your kind reply I will try to work on BBMAP. Cheers.

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updated by Ram Ram • written by nsknadendla • nsknadendla

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