Get gene names from genomic coordinates

Question

[Ander]

Hi pals!

I have a list of genomic coordinates in format [chromosome start end] from possible genes, I also have access to my bacterial genome of interest in several formats from NCBI ftp server. What I want to do is:

• Extract the systematic name of my sequence (e.g. VIBHAR_00334) in case it corresponds to a gene, and its orientation
• Extract the systematic names of the upstream and downstream genes of my coodinates and their orientation.

Are there any tools that can help me do this? I can browse my genome manually and search for this, but I have more than 200 sequences...

PS: I'm running 64bit Windows 7 and 64bit Ubuntu 14.01.

Answer 1

[chemcehn]

prepare files with your target regions and your bacterial genome in the BED format, and then apply

intersectBed from Bedtools

or

annotatePeaks from HOMER

[Ander]

Thanks for your help Chemcehn!

I've never heard of HOMER, but it sound great!! Could I run it by using my coordinates in BED format and match with my genome in FASTA + GFF formats? Like:

annotatePeaks.pl coordinates.txt genome.fa -gff genome.gff > output.txt

[chemcehn]

As far as I remember, you can install any new genome to HOMER, and then annotate your BED file with putative regions using annotatePeaks

[Bioinformatist Newbie]

Hi,

I have to map my reads with E.coli genome, I am not getting how I can install Escherichia coli str. K-12 substr. MG1655 genome in homer. Can you guide me how I can do that?