Finding genomic location of a list of sequences in human reference genome

Question

[User6891]

Hi everyone,

I'm trying to find the genomic location of a list of sequences in the reference genome. So if my sequence is 'ACGTACGTAGTCATGC', I want as an output something like this:

chr1  position of the first nucleotide   position of the last nucleotide

Are there any tools to do this? Blastn maybe? But since I have the reference genome locally installed, there might be some other options?

[Devon Ryan]

Do you only want exact matches? You can install blast locally, btw.

[User6891]

Yes indeed, only exact matches. About blast, indeed we have blast locally installed. But I'm not really experienced with blast. So I was wondering if there are other options.

Answer 1

[Devon Ryan]

If you only need exact matches, then give one of the answers in this thread a try: Locating A Sequence In A Fasta File.

[User6891]

If I wanted to use blast:

Do you think 'blastn' would work? With then as -db the human reference genome? My sequences are around 20bp long.

[Devon Ryan]

Sure, I'd expect so. That's probably faster once the index is made, though you'll need to build the index first. Of course if you only have to do this a couple times, then using one of the methods in the thread I listed is probably faster than building the blast database and filtering the results.

Answer 2

[Siva]

You can also use blat. Since your query sequences are shorter, you might also want to check Using Blat for short sequences with maximum sensitivity

Answer 3

[Vova Naumov]

An easy way is to use such mapping tool as bowtie. First you will need to index reference file using bowtie-build.

Than you can find location of your sequence using:

bowtie -c <reference.ebwt.prefix>  ACGTACGTAGTCATGC

this will give you coordinates of this sequence.

For more information look at http://bowtie-bio.sourceforge.net/tutorial.shtml