Question: How To Blast A Nucleotide Profile (Pssm) Against A Nucleotide Database?
1
gravatar for Panos
7.3 years ago by
Panos1.7k
Geneva, Switzerland
Panos1.7k 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
ADD COMMENTlink modified 7.3 years ago by Torst960 • written 7.3 years ago by Panos1.7k

Hi Panos,

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

ADD REPLYlink written 7.3 years ago by always_learning1.1k

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 REPLYlink written 7.3 years ago by always_learning1.1k

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

ADD REPLYlink written 7.3 years ago by Panos1.7k

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

ADD REPLYlink written 7.3 years ago by always_learning1.1k

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 REPLYlink written 7.3 years ago by Panos1.7k

I scanned sequences database with that Matrix !!

ADD REPLYlink written 7.3 years ago by always_learning1.1k

I scanned sequences database with that Matrix !!

ADD REPLYlink written 7.3 years ago by always_learning1.1k

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 REPLYlink written 7.3 years ago by Panos1.7k

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

ADD REPLYlink written 7.3 years ago by always_learning1.1k
5
gravatar for Torst
7.3 years ago by
Torst960
Australia
Torst960 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 COMMENTlink written 7.3 years ago by Torst960
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