fasta to stockholm

Question

[saadleeshehreen]

Hi,

I am trying to convert a fasta file (protein) to Stockholm formate by using the following site: http://sequenceconversion.bugaco.com/converter/biology/sequences/fasta_to_stockholm.php

But it generates an error message ( Sequences must all be the same length). My proteins are different length. How can I solve this problem?

Cheers

[finswimmer]

Hello saadleeshehreen,

if I understood the Stockholm format correct it is an alignment format. So to convert fasta to it, it is neccessary that the fasta sequence contains alignment characters to mark gaps between the aligned sequences. That said all sequences must have the same length.

The converter is not intended to do the alignment.

fin swimmer

[Joe]

Seems like an XY problem. What are you actually trying to do?