How to BLAST 400 genes against genome at once?

Question

[michael.nagle]

I have a list of 400 genes. I just need a way to BLAST all of them against a genome without doing it one at a time. I know on NCBI's site you can have input a list of genes if you're blasting them against each other, but I'm BLASTing against the genome.

Thanks for your help.

[Prasad]

You can do it using BLAST2. Give your all gene sequences as query and enter genome sequence/s as subject

[natasha.sernova]

See this post.

Mapping large contigs to a reference genome

Let's suppose your genome is a reference genome and your genes are contigs.

See also this post. You don't need blast.

A: What Are You Using For A Reference Assembler?

Only Bwa and Bowtie.

On the other hand Blast 2 (as Prasad suggested) may be easier.

Standalone Blast 2 Short Sequences

[MAPK]

Have you checked the command line option for BLAST?

[GenoMax]

Are you going to try to do this locally or at NCBI? If latter then @EagleEye has linked the relevant NCBI help page below.

If you are going to do this locally then keep in mind that depending on size of your dataset/reference you are using the search will not be trivial (in terms of hardware spec for computer).

Basic idea is to split your genes into a set of files (1 per or more) and then use a for loop like the one described in this post: blast running for several splitted query to go through the set of files.

[michael.nagle]

I'm new to command line and I would prefer to do this through NCBI if possible. I'm just starting to learn BioPython. Can this be done through NCBI?

I tried going through the link below from EagleEye. This blasted all 400 genes together instead of separately. I need to get the top 2 BLAST results for each of the 400 genes.

Answer 1

[EagleEye]

http://www.ncbi.nlm.nih.gov/guide/howto/submit-mult-seq-blast/