How to detect and visualize ORFs in bacterial genome?
0
0
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
ADD COMMENT
0
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?

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1993 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6