How to align the sequence with the 1000 Genome project?

[hylei]

Dear all:

I want to see whether I can find the target sequence in the 1000 genome project, especially in the non-human sequence. Does it any easy way that i can search the database just like running the blast against nr database? Thanks very much.

HY

[GenoMax]

http://www.1000genomes.org/faq/can-i-blast-against-1000-genomes-data-sets

What exactly are you looking for?

[hylei]

Thanks very much for your reply. I really want to find some target sequence in the non-human sequence in the 1000 Genome project. Can you please give me some idea how I can do it? Thanks.

HY

[GenoMax]

I have heard about mycoplasma contamination (http://www.biodatamining.org/content/7/1/3). What other non-human sequences are you expecting to find?

[hylei]

We want to find the bacteria sequence. Can you give me some idea the easy way to search the 1000 Genome project? Thanks.

HY

[GenoMax]

"Bacteria" is probably too broad a space to go searching.

You can use the search strategy from the paper I linked above. I doubt that there is an "easy way" to search. It would be best to refine the search question before you go diving into 1000 genomes data