How to BLAST 400 genes against genome at once?
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.
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EagleEye
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michael.nagle
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michael.nagle
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You can do it using BLAST2. Give your all gene sequences as query and enter genome sequence/s as subject
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
Have you checked the command line option for BLAST?
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
forloop like the one described in this post: blast running for several splitted query to go through the set of files.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.