Aligning full length primary transcripts to a reference genome

Question

[mmaselko]

My goal is to retrieve the promoter regions of a few hundred genes. I have the primary transcripts of these genes in a FASTA file and the organism's genome in another FASTA file.

How can I align the transcripts to the reference genome and then retrieve 200nt of genomic sequence upstream of the transcript?

Thanks for the help!

Answer 1

[Vivek]

You could use Blat to align the transcripts to the genome, once you have the coordinates, you could create a bed file of 200 nt upstream of the alignment start and use getFasta of BedTools suite to retrieve the promoter sequence from the reference genome.

http://bedtools.readthedocs.org/en/latest/content/tools/getfasta.html

Answer 2

[Prakki Rama]

In addition, you can also use GMAP to align the transcripts to genome. Check this tutorial for more information.