Acquiring very large nucleotide sequence in matlab workspace.
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I have been facing the following problems while trying to import very large amt of data in the form of a sequence(~MBases). 1.Using getgenbank does not load the sequence information and CDS headers into Matlab so Iam unable to access some sequences.(Matlab version r2009a) 2. If i use seqtool for a very large sequence eg 'NC_00091', Matlab stops responding. 3. If somehow I am able to access very very large sequences into workspace for some of the organisms using genbank or seqtool, while trying to run the code, matlab exits automatically. And sometimes it shows an error saying data is too large. 4. Do I need to use a bioindexed file for this purpose? Or am I missing out on the memory management part?
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the cyclist
am 6 Mai 2012
Can you give a sense of how large "very large" is? How many numbers would you need to store, and what is the nature of those numbers (e.g. are they small integers, or double-precision, etc)?
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Diego
am 6 Mai 2012
What are you trying to accomplish?
The first I'd do is to watch this webinar: Large Data Sets in MATLAB
Other options for handling contig sequences would be:
- -. kent's source tree tools
- -. bioperl
Just my 2 cents,
Regards,
Diego
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