Saturday, March 24, 2007

An additional function for NCBI Blast?

One problem that users face when using the good ol' NCBI to blast short sequences is that the result excludes inverted sequences. Inverted sequences are of interest to molecular biologists studying the activity of promoter sequences. Molecular biologists intending to study different mutations in genes during the course of evolution might be interested in inverted mutations within the genes of study.

Assuming the user wants to BLAST the sequence 5-aggatttcat-3
Result 1:5"---//-aggatttcat---3" Result 2: 5"----//-tactttagga---3"

He would more likely have obtained Result 1. Perhaps inverted mutations can be picked up with the following algorithm:
1) Generate two short sequences for alignment 5"-aggatttcat-3" and 5"-tactttagga-3"
2) Align the upstream and downstream sequences for the hit results obtained for the two short sequences against one another to confirm an inversion mutation.

5"-aggagttgcaggatttcataaggtta-3" 5"-aggagttgctactttaggaaaggtta-3"

For instance, an inversion mutation occured in the above sequence. The upstream and downstream sequences of the two sequences are perfectly aligned with each other except for the short sequence, which is inverted.

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