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Question: How To Blast A Nucleotide Profile (Pssm) Against A Nucleotide Database?
1
gravatar for Panos
7.3 years ago by
Panos • 1.7k
Geneva, Switzerland
Panos • 1.7k wrote:

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!
pssm blast blastn • 4.0k views
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modified 7.3 years ago by Torst • 960 • written 7.3 years ago by Panos • 1.7k

Hi Panos,

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

ADD REPLY • link written 7.3 years ago by always_learning • 1.1k

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 !! :) :)

ADD REPLY • link written 7.3 years ago by always_learning • 1.1k

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

ADD REPLY • link written 7.3 years ago by Panos • 1.7k

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

ADD REPLY • link written 7.3 years ago by always_learning • 1.1k

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?

ADD REPLY • link written 7.3 years ago by Panos • 1.7k

I scanned sequences database with that Matrix !!

ADD REPLY • link written 7.3 years ago by always_learning • 1.1k

I scanned sequences database with that Matrix !!

ADD REPLY • link written 7.3 years ago by always_learning • 1.1k

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

ADD REPLY • link written 7.3 years ago by Panos • 1.7k

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

ADD REPLY • link written 7.3 years ago by always_learning • 1.1k
5
gravatar for Torst
7.3 years ago by
Torst • 960
Australia
Torst • 960 wrote:

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.
ADD COMMENT • link written 7.3 years ago by Torst • 960
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