How to get chromosomal coordinate of blasted genomic fragment?

Question

[Wet&DryImmunology]

Hi, I have a very rudimentary question. I am interested in a genomic fragment with known chromasomal coordinate. I wanna load the fragment in my genome browser (IGV) together with other tracks. I know that what I could do is simply to create a bed file with coordinates of this genomic fragment. but how could I get the coordinates? I could blast the fragment, but how to get the chromosomal coordinates? like:

chr1 10027418 10028924 MACS_peak_12 2462.42

Thanks!

[venu]

You can use BLAT from UCSC.

[Wet&DryImmunology]

@venu, Thank! Issue solved!

[Denise CS]

Ensembl has also got its BLAST/BLAT tool if you want to give that a go. See our tutorial video. You can search for your sequence and view the similarity results on the genome browser with all the annotation from Ensembl which includes our own annotation of genes and transcripts, variation data from dbSNP, ExAC, 1000 Genomes with their effect on proteins and transcripts; data from ENCODE, Blueprint, Roadmap as part of our regulatory build and comparative genomics data as well. We also provide a rather cool image showing the hits on the karyotype (aka HSP distribution on genome).