ORF (open reading frame) finder for genome
6 views (last 30 days)
Show older comments
Dear Sir,
I need to generate a set of all possible ORFs (4 codons or longer)
in the entire genome for some microbial sequences, for that I used
“SEQSHOWORFS “ Function from Bioinformatics toolbox and got the
following error :
“SEQSHOWORFS can only display at most 1000000 symbols. Use
“SEQTOOL” to display ORFs for long sequences or use a shorter sub-
sequence or fewer reading frames”.
Since “SEQtool” is only ORF visualization tool, How can we take
out the identified ORFs into a separate file for the further
analysis?
Thank you so much in advance sadaf
1 Comment
N/A
on 19 Nov 2011
Hi Sara!
Did you discover how to obtain ORFs for long sequences into a separate file?
I have the same problem here!
=/
Thanks!
Answers (2)
Stephanie Logan
on 9 Oct 2018
if you go into edit seqshoworfs.m it opens the file. Read through it and find where it restricts the limit. It says it causes a Java issue but I added two zeros and had no problem. Took some time but worked.
0 Comments
Achal Mahajan
on 1 Jun 2022
Edited: Achal Mahajan
on 1 Jun 2022
Hi,
You can use seqviewer app to visualize the base pairs if the size of the genome > 1000000. The app also generates a set of all possible ORFs, complement sequence and reverse complement sequence as well.
A random sequence is generated here using the in-built function randseq.
Here is a sample script to do that:
-Achal
clear all;clc;close all;
s = randseq(1000000, 'alphabet', 'dna');
seqviewer(s)
0 Comments
See Also
Categories
Find more on Genomics and Next Generation Sequencing in Help Center and File Exchange
Products
Community Treasure Hunt
Find the treasures in MATLAB Central and discover how the community can help you!
Start Hunting!