Question: mpiBLAST Score and E-value Calculation
0
gravatar for Lakshman Rao
5.2 years ago by
India
Lakshman Rao0 wrote:

Hi..

Can anyone help me how to calculate the score and E-value in BLAST protein sequencing.

Also kindly help how to calculate the E-values in decimal format.. Example: value of 4e-04 ?

Thank You in advance

blast sequence • 1.4k views
ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 5.2 years ago by Lakshman Rao0

What do you mean by calculating. The actual formula is (AFAIK) the same as you have in nucleotide blasts which is explained here (wikipedia...)

4e-04 == 0,0004 == 4 * 10^-4

Is that what you wanted?

 

HTH

 

 

ADD REPLYlink written 5.2 years ago by Phil S.660

Dear,

Thank you for giving support with your reply..

Can You please help me in execution of Hadoop BLAST .

Thank you in advance.

Thanks & Regards, P. Lakshman Rao Ph. No. 8099596331

ADD REPLYlink written 5.2 years ago by Lakshman Rao0

To help you using blast (on whatever system) you need to ask more specific question, what do you mean by 'execution of blast on Hadoop?'. Although I don't use Hadoop I can try if you give some more information what you want to do...

 

ADD REPLYlink written 5.2 years ago by Phil S.660

Dear Phil,

Sequencing of the proteins can be done by using BLAST. For our convenience we are doing that operation parallely using number of processors nothing but "mpi BLAST" Like that only we can also use "Hadoop- MapReduce", which is a distributed programming to perform BLAST.

Thanks & Regards, P. Lakshman Rao Ph. No. 8099596331

ADD REPLYlink written 5.2 years ago by Lakshman Rao0

First of all, I highly doubt that you actually sequence proteins using blast!! What you do is you map your AA sequence back to some database.

Therefore have a look at the makeblastdb command coming with your local installation of blast, i.e.

makeblastdb -dbtype prot yourDatabase.fasta

 

after that you can blast this database using for example

blastp -db yourDatabase.fasta -query yourProteinAAsequences.fasta -outfmt 6 -out ./yourOutputFilet.txt

 

which will give you your results in the file yourOutputFilet.txt in the directory you are currently located. IIRC you just need to adapt this by using your hadoop batch / queue and your are all set.

 

HTH

ADD REPLYlink written 5.2 years ago by Phil S.660

Dear Phil,

Actually I want to write BLAST Sequence code in C or Java Programming Language.

I mean that to write the code, how exactly BLAST algorithm works.

Is the code is available? If it is, how can I download and execute.

ADD REPLYlink written 5.2 years ago by Lakshman Rao0

this is the official blast website. You can download precompiled binaries etc. from there. But I don't know if you can also download the source....

ADD REPLYlink written 5.2 years ago by Phil S.660

Dear Phil,

I cited BLAST tutorials, NCBI, other website to learn how to calculate the Score and E-value.. But I am not able to understand.

I will explain the example I done... After BLAST between the Query ( Length=92) and Subject ( Length= 130), the values are:

Identities= 7/27(25%) Positives= 14/27(51%) Method: Compositional Matrix adjust Score= 16.9 bits(32) E-value= 0.082

Based on Identities, positives and lengths of Query, subject,, How can I calculate Score and E-value..

Kindly help me...

Thanks & Regards..

P. Lakshman Rao (M.Tech Student), University College of Engineering, J.N.T.University, Kakinada, Andhra Pradesh, India

Ph. No: +91 8099596331

ADD REPLYlink written 5.1 years ago by Lakshman Rao0

Maybe you can have a look into this where it is really well explained!

 

ADD REPLYlink written 5.1 years ago by Phil S.660

Thank You so much..

Thanks & Regards..

P. Lakshman Rao (M.Tech Student), University College of Engineering, J.N.T.University, Kakinada, Andhra Pradesh, India

Ph. No: +91 8099596331

ADD REPLYlink written 5.1 years ago by Lakshman Rao0

you are welcome!

 

ADD REPLYlink written 5.1 years ago by Phil S.660

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