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Get gene names from genomic coordinates

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.

genome gene sequence
• 4,988 views • link
updated by chemcehn chemcehn • written by Ander • Ander

1 answer

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

intersectBed from Bedtools

or

annotatePeaks from HOMER

• 1 views • link
written by chemcehn chemcehn

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
• 1 views • link
updated by Ram Ram • written by Ander • Ander

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

• 1 views • link
updated by Ram Ram • written by chemcehn chemcehn

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