mpiBLAST Score and E-value Calculation

Question

[Lakshman Rao]

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

[Phil S.]

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

[Lakshman Rao]

Dear,

Thank you for giving support with your reply..

Can you please help me in execution of Hadoop BLAST

Thank you in advance

[Phil S.]

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...

[Lakshman Rao]

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.

[Phil S.]

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

[Lakshman Rao]

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?

[Phil S.]

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....

[Lakshman Rao]

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...

[Phil S.]

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

[Lakshman Rao]

Thank you so much

[Phil S.]

You are welcome!