How To Blast A Nucleotide Profile (Pssm) Against A Nucleotide Database?
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10.6 years ago
Panos ★ 1.8k

I saw that tblastn is capable of doing that kind of search, but I want my position-specific scoring matrix (pssm) to be built from nucleotide, not protein, sequences.

Has anyone done something similar before?

Thanks!

blast pssm blastn • 5.4k views
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Hi Panos,

I have used Prophecy tools from Emboss package for something similar task !! You may have a look on that.

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To add more , Prophecy create matrix based on 1. Gribskov 2. Henikoff 3. Frequency method too. I have used this long before during my master's thesis !! :) :)

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Thanks a lot! I guess that after you create the pssm with Prophecy, you feed this to tblastn, right?

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No !! First I did the alignments of sequences ( In my case we have transcription binding sites region) and then we created the matrix. .

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So what did you do with the matrix? In my case, I want to blast it against a nucleotide database. Did you also do something like this?

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I scanned sequences database with that Matrix !!

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I scanned sequences database with that Matrix !!

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I'm guessing you haven't used the matrix for searching a BLAST-formatted, nucleotide database, right? If you did, what program you used?

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I used the Profit for scanning the Matrix with Sequences !! These sequences are 500 Upstream of IdeR Transcrition binding withing species of MTb !!

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10.6 years ago
Torst ▴ 980

You have a nucleotide PSSM and want to scan it against a database of nucleotide sequences?

Option 1: PoSSuM - excellent fast optimized PSSM scanner http://bibiserv.techfak.uni-bielefeld.de/possumsearch

Option 2: Instead of a PSSM, use the same alignments to build a nucleotide HMM and use NHMMER from HMMER 3.1-dev http://hmmer.janelia.org/

Option 3: Turn it around and use RPS-BLAST (rpsblastn from BLAST+) using your PSSM as the database and the sequences as your query.

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