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How am I supposed to view/handle really long nt sequences on NCBI?


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#1 humalog

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Posted 04 May 2011 - 11:32 PM

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?

#2 humalog

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Posted 05 May 2011 - 02:48 AM

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.


#3 HomeBrew

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Posted 05 May 2011 - 01:58 PM

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.

#4 humalog

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Posted 07 May 2011 - 09:42 AM

Thanks HomeBrew I am processing your reply now.




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