Obtaining random excerpt from DNA sequences

[matthend]

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

[jonmoulton]

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.

[JackBean]

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...

[matthend]

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

[JackBean]

basically you can, but *.fasta is IMHO better

[matthend]

Modulo bandwidth fines it isn't!

[JackBean]

?

[matthend]

The downloads are too big, on my connection I'll get fined if I go over 1GB in one day

[mith]

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?

[matthend]

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

[JackBean]

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

[matthend]

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