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Obtaining random excerpt from DNA sequences

Genetics as it applies to evolution, molecular biology, and medical aspects.

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Obtaining random excerpt from DNA sequences

Postby matthend » Fri Jan 15, 2010 4:22 pm

Hey all,

I am doing a project for which it would be useful to obtain say a 100KB text file of A, C, Gs and Ts corresponding to a random excerpt of an organism's DNA sequence.
I have had a look at various websites including http://genome.ucsc.edu/, but I can't seem to download the type of file I want.

So ideally I'd like to obtain such a text file for a selection of animals taken from anywhere in their DNA.

Any ideas for how this can be done?
Thanks,
Matt
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Postby jonmoulton » Fri Jan 15, 2010 4:30 pm

Try:
http://www.ncbi.nlm.nih.gov
searching the nucleotide database.

Also try:
http://www.ensembl.org

You can copy a nucleotide sequence and paste it into a text file.
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Postby JackBean » Fri Jan 15, 2010 4:31 pm

Look for their FTP server like here
http://www.maizesequence.org/index.html
on top right is BLAST/login/bla/FTP/Archive/...
so you can get here
http://ftp.maizesequence.org/current/
where y\ou can download sequences, you like...
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Postby matthend » Fri Jan 15, 2010 4:33 pm

Thanks-
I guess I can use pages like this:
http://www.ensembl.org/Homo_sapiens/Loc ... 2-22112083

And copy and paste into text files
M
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Postby JackBean » Fri Jan 15, 2010 4:35 pm

basically you can, but *.fasta is IMHO better
http://www.biolib.cz/en/main/

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Postby matthend » Fri Jan 15, 2010 4:39 pm

Modulo bandwidth fines it isn't!
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Postby JackBean » Fri Jan 15, 2010 4:54 pm

?
http://www.biolib.cz/en/main/

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Postby matthend » Fri Jan 15, 2010 4:55 pm

The downloads are too big, on my connection I'll get fined if I go over 1GB in one day
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Postby mith » Fri Jan 15, 2010 5:09 pm

it would be more helpful if you could give us more details on your project. 1gb is a lot of data how many seqs do you need? Can you just generate the seqs?
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Enjoying one moment at a time;
Accepting hardships as the pathway to peace;
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Postby matthend » Fri Jan 15, 2010 5:12 pm

I managed to use ensembl.org to take 128KB strings of A, C Gs and Ts from random positions in the sequences of:
a human, a bush baby, a chimpanzee, a rat, a cat, a chicken, an anole lizard and a zebra fish.
That'll help in my project.
If these files would be useful to anyone else, do get in touch.
Matt
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Postby JackBean » Fri Jan 15, 2010 5:17 pm

Then just go to www.pubmed.com and under nucleotide look for genome. There you can easily access them from all species and in fasta format
http://www.biolib.cz/en/main/

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Postby matthend » Fri Jan 15, 2010 5:20 pm

I've already done it,
thanks for the help.
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