How to batch download thousands of FASTA files?

[J:Mo]

Hi All

I'm conducting an in silico analysis on genes of interest highlighted by a human microarray study. I need to download full-length protein sequences for ~2000 gene products as FASTA files. Currently I am faced with the prospect of individually searching the GenBank database which promises a mental breakdown. Are there any available programs I can use to do this quickly?

Thanks for any suggestions

Joe

[maubp]

How about just downloading the complete gene set as FASTA, and then filtering it locally? That should be much easier and less prone to network failures likely if you try ~2000 queries online.

[kmcarr]

Not a program but a set of tools, the NCBI E-Utilities. For example Application #2 on that page shows how to retrieve FASTA files from a list of protein accession numbers. That application only supports retrieving a few sequences at a time but it points to other examples on that page to extend the application for a larger number of sequences.

[GenoMax]

Joe: If you have the identifiers available in a file, then you may want to do this using the BioMart tool at http://www.ensembl.org. Click on the BioMart link at the top. There are tutorials available for BioMart if you have not done this before.

You can also use the Table Browser at UCSC (a bit more non-intuitive) or Galaxy (http://usegalaxy.org) and its "Get Data" function.

If you strictly need the sequences in independent files (not sure of why you would need this) then you will need to split them.

[J:Mo]

Cheers all - really helpful. Another way I found is to use Batch Entrez and select the FASTA as text output format. Every day's a school day!?!

[gopi1616]

Fasta sequence batch download for a list of protein names

Cheers all - really helpful. Another way I found is to use Batch Entrez and select the FASTA as text output format. Every day's a school day!?!

I need fasta sequences for list of proteins, In batch entrez it requires GI or accession number to retrieve sequence but I only have protein names! how can I get the sequences can somebody help me out!

[GenoMax]

Are these names from a single organism?