How to extract conserved regions from multi sequence alignment by linux terminal?

Question

[Ahmad]

Hello everyone, I hope you are well I want to make common PCR primer for group of sequences , So I want to extract conserved regions from multi sequence alignment by linux terminal. Is there a tool or loop that can help me with that?

Thanks for your attention

[Mark]

I realise your question is about finding conserved region but your main task is primer design. So why not use a tool dedicated to designing primers? eg primer3/primerblast?

[Ahmad]

I think that these tools do not work on the conserved regions or similar regions in the sequences, but here they work individually on each sequence, and do not produce a common primers

[shenwei356]

http://trimal.cgenomics.org/introduction

[Ahmad]

Thanks, but

I need command line not GUI

[shenwei356]

It does provide command-line interface: http://trimal.cgenomics.org/use_of_the_command_line_trimal_v1.2

[Ahmad]

Ok, thank you I will try

Answer 1

[Joe]

You could relatively simply adapt code like here: Trim sequences based on alignment in python

Instead of searching for the first non-gap character, you could simply substitute in a test that checks if every character in a given column is the same.