Effect of BLAST Low complexity filter on BLAST Results
This post is regarding one of my recent experiences with BLAST. I was trying to blast a big fasta file consisting of sequences over 4000 base pairs in length, and had the low complexity filter turned on (which is always ON by default).
Ideally when you blast a sequence against itself, it should give you a match over the entire length, but in this case for a sequence of 4200 bp, it only gave me a match over 1500 bp. This is what perplexed me for some time, and I decided to research this problem using NCBI's "blast2seq" tool, with both input sequences same as the 4200 bp sequence. This gave me 3 hits over lengths ranging from 1500 to 1200 bp. This gave me a clue to turn the filter "off", and then I found the hit to be over the entire region.
I hope someone facing the same problem would benefit from this post :)
Best.
Puneet Wadhwa
Ideally when you blast a sequence against itself, it should give you a match over the entire length, but in this case for a sequence of 4200 bp, it only gave me a match over 1500 bp. This is what perplexed me for some time, and I decided to research this problem using NCBI's "blast2seq" tool, with both input sequences same as the 4200 bp sequence. This gave me 3 hits over lengths ranging from 1500 to 1200 bp. This gave me a clue to turn the filter "off", and then I found the hit to be over the entire region.
I hope someone facing the same problem would benefit from this post :)
Best.
Puneet Wadhwa
posted by Puneet Wadhwa at
1:55 PM
1 Comments:
Hi Puneet, Im facing a real problem with stand alone blast,,,,, and the script what I designed, which should run all the three blasts, that is blastn, blastp, tblastx, on requirement of the user using a genbank file. Thus, if you can help me out with the issue, will be ever grateful
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Unknown, at 10:07 AM
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