How would you BLAST a large de novo dataset to NCBI?

[grassgirl]

Hello forum members,

I am beginning sequence analysis on de novo cDNA libraries using the 454 Junior. I am wondering what I can do as far as BLASTING my contigs (or would I blast the isotigs?).

I know some folks use downloaded specific databases and run BLAST algorithms on clusters, but a researcher here in the past wrote a script to BLAST a large dataset from a desktop in small batches at a time.

I'm not fluent in the bioinformatics programming languages (yet), but have access to a computational cloud and would like the option of BLASTING on NCBI's site as opposed to a subset of databases which have been downloaded.

Anyone have any suggestions for how to do this?

Thanks,
Vicky

[maubp]

You can write scripts to BLAST against the NCBI database online at the NCBI, but doing this for 1000s of sequences will (a) take a long time, and (b) may annoy the NCBI and get you blocked.

Instead, you can download the NCBI blast tools and the NCBI BLAST databases and run the search locally. For the bigger databases (e.g. NT and also NR) you'll need a fair amount of disk space and RAM.

It is very likely that your local IT team already have a local copy of BLAST and the NCBI databases, since this is a common request. Ask them

[grassgirl]

Thank you, I did find out that, yes, we do have BLAST programs and databases on our cluster.