BLAST Help! - (Oct/24/2005 )

Hi all,

I'm trying to see if my novel sequence's location on any of the human/mouse/rat chromosomes. Please can anyone tell me how to do that.. I've tried MapViewer but couldnt understand how to go about it..

-Viku-

go to blast's website

go to a function called "blastn"

paste in your sequence to the little box

set filters for species of your choice (I doubt you will need other filters at this point; I would recommend the defaults)

hit the 'go' button

hit the 'format' button on the new screen; wait for your alignments and scores

GOOD LUCK!!

-aimikins-

QUOTE (aimikins @ Oct 24 2005, 08:28 AM)

Hello aimikins (Veteran),

I've just tried that but to no avail. It is not giving me what I was looking for.

Thanks anyway..

Viku

-Viku-

Try describing again for us what you're trying to do... If your sequence is "novel", why would you expect to find it elsewhere?

-HomeBrew-

QUOTE (HomeBrew @ Oct 27 2005, 03:49 AM)

Try describing again for us what you're trying to do... If your sequence is "novel", why would you expect to find it elsewhere?

I've found, after differential display work, a novel sequence and now I want to find out its chromosomal location in either rat/human/mouse. I've used BLASTn program for all the other sequences which I've got. Similar work is done by a group and they did identify the location of their novel sequence, but they didnt explain how they found. So I dont know what to make of it..

-Viku-

Try using the NCBI blast functions against specific sequences:
http://www.ncbi.nlm.nih.gov/genome/seq/MmBlast.html -> in this case the Mouse... there are also human etc.

Or perhaps ensembl
http://www.ensembl.org/Homo_sapiens/blastview

-DPK-

Hi DPK,

Well, I think the idea of using the ensembl.org did help very much, though it did solve some basic questions... So many thanks to you for that suggestion.. Thanks once again..

Viku..

QUOTE (DPK @ Oct 27 2005, 08:45 AM)

-Viku-