Annotations in multiple sequence alignments?

Question

[gasparsanchez]

Dear all,

first of all I want to apologize for my lack of knowledge and unfamiliarity with the bioinformatic workflows. I'm looking for a program or online tool that allows to make annotations on individual sequences in an alignment file.

Basically, I need to compare short genomic regions from different populations of the same species, in which small variations at the DNA sequence have caused rearrangements of the exon/intron structure of the genes coded in those regions. So I need to annotate each population's sequence individually and align them so that the mutations causing the rearrangement in each population are easily noticed.

I'd be very grateful for any recommendation.

[GenoMax]

Jalview is another option you can use.

[gasparsanchez]

I'm not that familiar at all, but I'm afraid I'll need to go through it sooner or later... Thank you for your answer!

Answer 1

[Joe]

I'm guessing if you're a beginner you aren't all that familiar with LaTeX, but TeXShade is an option. You can take a look at this previous thread:

Is there a command line tool that can take an alignment fasta and input and outputs an image?