ORF (open reading frame) finder for genome

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

[Vinícius Marques Stocco]

Hi Sara!

Did you discover how to obtain ORFs for long sequences into a separate file?

I have the same problem here!

=/

Thanks!

Answer 1

[Stephanie Logan]

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.

Answer 2

[Achal Mahajan]

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)