How to detect and visualize ORFs in bacterial genome?
Entering edit mode
5 weeks ago

I got the consensus sequences from a couple of my bacterial isolates. I generated the VCF files, and one has about 83 SNPs and the other over a thousand. I would like to check if these SNPs have affected the coding potential of the strains.

Is there a program to visualize the ORFs of these isolates? I know of Artemis, but the map I get is a bit raw, for I can't see all the ORFs at once, and it is a little informative. In the figure below, I can see a portion of the genome, not all of it and I don;'t know how to fix the view to all the genome:

enter image description here

(Also, how can I load the annotations?)

Is there a way to determine the number of ORFs to see if some of them are missed over the reference genome? I know of Augustus, but I get a textual output like this:

# ----- prediction on sequence number 1 (length = 4598762, name = K-12_Ho) -----
# Predicted genes for sequence number 1 on both strands
# start gene g1
K-12_Ho AUGUSTUS    gene    70  1404    1   +   .   g1
K-12_Ho AUGUSTUS    transcript  70  1404    1   +   .   g1.t1
K-12_Ho AUGUSTUS    start_codon 70  72  .   +   0   transcript_id "g1.t1"; gene_id "g1";
K-12_Ho AUGUSTUS    single  70  1404    1   +   0   transcript_id "g1.t1"; gene_id "g1";
K-12_Ho AUGUSTUS    CDS 70  1404    1   +   0   transcript_id "g1.t1"; gene_id "g1";
K-12_Ho AUGUSTUS    stop_codon  1402    1404    .   +   0   transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtggatac...

that is difficult to handle (I'll have to write a script to extract statistics from it). Is there something more straightforward?

Thank you

statistics visualization ORFs genome • 258 views
Entering edit mode

Why not use IGV, if you have the GTF/GFF files and the reference these were aligned to?

I can't see all the ORFs at once

That is going to be the case with any visualization program, is it not?

Entering edit mode

I was hoping for something a bit more advanced than IGV but I reckon you are right: classic is better


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