Question: Blast Contigs To A Reference Sequence And Obtain An E-Value
0
gravatar for ant0422ant
5.1 years ago by
ant0422ant0
ant0422ant0 wrote:

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....

assembly alignment blast • 3.2k views
ADD COMMENTlink modified 5.1 years ago by Rohit1.3k • written 5.1 years ago by ant0422ant0
2
gravatar for Neilfws
5.1 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink written 5.1 years ago by Neilfws48k

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!!

ADD REPLYlink written 5.0 years ago by ant0422ant0
1
gravatar for chefer
5.1 years ago by
chefer260
Pretoria, ZA
chefer260 wrote:

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.

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by chefer260
1
gravatar for Jeremy Leipzig
5.1 years ago by
Philadelphia, PA
Jeremy Leipzig17k wrote:

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/

ADD COMMENTlink written 5.1 years ago by Jeremy Leipzig17k

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

Thanks so much for the answer!!!

ADD REPLYlink written 5.0 years ago by ant0422ant0
1
gravatar for Rohit
5.1 years ago by
Rohit1.3k
European union
Rohit1.3k wrote:

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.

ADD COMMENTlink written 5.1 years ago by Rohit1.3k

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

ADD REPLYlink written 5.0 years ago by ant0422ant0
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