3 replies to this topic

[humalog]

Hi.
Say that I want to run a really long sequences through some bioinformatics software.
If I find this sequence on NCBI nucleotide, for example, and press on FASTA to view its sequence, the NCBI site takes ages to download/show the sequence, because its reallllllly long.
Also, even if it did download (something that didn't happen because I never had the patience for) I'm not sure whether I'd be able to copy such a long sequence on my clipboard, and then how would the other bioinfo software be able to process such a long sequence.
Is there an easier way to handle so large sequences?
I'm thinking whether I could download the FASTA sequence as a file instead? Would that make any difference? And how would I go about doing that?

[humalog]

Another thing, is it just me or has the NCBI Nucleotide turned VERY much slower than what it was about 1 year ago, in terms of retrieving nt sequences.
I've noticed this on two different otherwise-fine internet networks.

I don't even have the patience to wait for a sequence to download (it takes several minutes) while the same sequence would download in a few seconds some months ago.

Edited by humalog, 05 May 2011 - 02:49 AM.

[HomeBrew]

You can download the data by FTP -- see here, for example, for bacteria. Another good spot is the Kyoto Encyclopedia of Genes and Genomes (KEGG), see here.

[humalog]

Thanks HomeBrew I am processing your reply now.