Blast Contigs To A Reference Sequence And Obtain An E-Value

Question

[ant0422ant]

Well, I'm a newbie of blast, so...hope I'm not asking a stupid question....

I've already have a set of contigs which is done by de novo assembler. Format of these contigs is fasta. Now I want to align these contigs to a reference sequence by using blast. And obtain only single e-value or a value shown the similarity between contigs and reference sequence.

I used blastn on linux system with "-subject reference.fa" command, but it only showed identity and e-value for each contig. And it would be problematic for summarizing these values.

So, is it possible for blast to do such a job? I mean, calculate a single value which can present similarity between contigs and reference sequence.

I've searched for hours and can't seem to find a straight answer. Please do help me....

Answer 1

[Neilfws]

You're aligning multiple query sequences to one reference. A single measure of similarity for multiple queries does not make sense. So the answer is: you don't want to do that, using BLAST or anything else.

[ant0422ant]

Well, I just want to calculate how similar between contigs I assembled and the reference. I think there are still some metrics which can complete the task~ Anyway thanks a lot!!

Answer 2

[chefer]

Maybe the best would be to generate a density plot or histogram of the e-value distribution from all the assembled contigs? BLAST does not have the functionality you describe.

Answer 3

[Jeremy Leipzig]

You could use BLAST -m8 output and tabulate the bit scores - that might be a somewhat meaningful metric but it wouldn't really stand up to scrutiny

perhaps MAUVE would give you some kinda single metric: http://gel.ahabs.wisc.edu/mauve/

[ant0422ant]

I will give a try on using MAUVE. And is "BLAST -m8" used on blastall?

Thanks so much for the answer!!!

Answer 4

[Rohit]

First thing is there is nothing called a stupid question.

The tabular outfmt 7 of blast combined with pident (check the stand-alone manual), gives best results but do use the bit scores for comparison.

If you would like to use the results for further data merging then I guggest you to use XML output (outfmt 5) and then parse whatever you need.

[ant0422ant]

And I've tried these two formats, but too many results to summarize. Anyway thanks your answer!! B-)