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ORF (open reading frame) finder for genome

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Sara Kamali
Sara Kamali 2011-7-1
编辑： Achal Mahajan 2022-6-1
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 个评论
N/A
N/A 2011-11-19
Hi Sara!
Did you discover how to obtain ORFs for long sequences into a separate file?
I have the same problem here!
=/
Thanks!

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回答（2 个）

Stephanie Logan
Stephanie Logan 2018-10-9
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.
Achal Mahajan
Achal Mahajan 2022-6-1
编辑：Achal Mahajan 2022-6-1
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)

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