Blast A Specific Contig Against Multiple Contigs From Another Organism

Question

[Ben Martin Ndsu]

I have a contig from one organism that is of interest. I have been searching this contig against another organisms complete collection of contigs found on NCBI by using an online DNA translator and BLAST (bl2seq) to do so. There are several hundred pages of these and I am wondering, Is there a way to blast all of them at once? I have gone as far as splicing many together through the translator, but top out at 500,000 characters, and the method does not really increase efficiency.

[John St. John]

What are you doing with the online translator? Also you can make a blast database of your contig collection (in fasta format) and search against that.

[Ben Martin Ndsu]

The online translator acts to remove spaces and other characters from the sequence once opened from NCBI data base, allowing me to insert it into the BLAST alignment. Let me clarify that I just started doing this as an undergrad research assistant. I am unfamiliar with much of the tools available. I am trying to streamline a process that was defined to me by another researcher in the lab. What is FASTA format? and how do I go about creating the database? Thank you so much!

Answer 1

[ALchEmiXt]

It depends on the number of contigs you would like to BLAST. If these numbers are high I think there are restrictions on doing that on the public NCBI servers.

A local blast+ installation is simple (get it from NCBI for your platform) and as mentioned by John, you can compare sets of query sequences against a formatted (downloaded) NCBI database or against your own multi fasta formatted sequences you got from elsewhere. Probably this is more convenient since you can easily restrict your number of hits and let the output be tabular (or xml if you want all details) for later parsing. More info in the extensive help sections of NCBI.

Fasta can be found here.

[Ben Martin Ndsu]

Thanks! I did find a way to do what I wanted, but only because I got lucky. BLAST allows you to search a sequence against a whole shotgun genome, if NCBI has it in their database. I simply pasted the sequence in selected the organism to search again and poof*, I had my matches! table 3.3 here http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=ProgSelectionGuide lists all the genomic databases you can search against!