Mapping two sequences to genome - (May/24/2005 )

Hi all,

Wondering if anyone knows of a free ware program that allows you to map two sequences against the human genome and get a graphical representation of the relationship of the two.

Scott

Hi Scott,

How far are the two sequence apart? You can try UCSC genome blat search at http://genome.ucsc.edu/cgi-bin/hgBlat?hgsid=42190156

You can format the two pieces of sequences as FASTA file like this
>Fragment_1
ccggttcccccaaact........
>Fragment_2
gcccgttccgaaatt.......

Paste the above to the input box and you will get matches to individual fragment. Then click "browser" (match to any fragment) you will be brought to the graphical display. Then click zoom out until you see both fragments in the graph aligned to the genome sequence. The following is an example I got from UCSC blat. My query sequences are marked as Fragment_1 and Fragment_2.

Or you can just stick two sequences into one piece and feed it into the query box.

Thanks PCRman,

I had been mucking around with the BLAT server and UCSC but didn't relise there is a zoom out function. I'll give it a go. The sequences are closely related and hit the same chromosome about 30,000 bases apart. I only really want the graphical representation for a presentation I have to give.

Cheers,