1
$\begingroup$

Given a set of genes in a FASTA-formatted file, for example: exFasta.fa, what is the best way to determine how well conserved the genes in that file are among an order of organisms, for example: Orthoptera?

BLAST is an obvious option, but I am not sure that it is the most efficient way considering there are likely thousands of organisms in that order. OrthoFinder also comes across as a valid option, but I am not sure how to implement such a thing considering the required inputs.

Any advice would be greatly appreciated!

$\endgroup$
2
  • 1
    $\begingroup$ Are these annotated, known genes? Or do you also need to detect/identify the potential homologs in the target species? $\endgroup$
    – terdon
    Commented Mar 16, 2023 at 12:43
  • $\begingroup$ Orthoptera (grasshoppers, crickets, locust) will be annotated (mostly). What they want to do is skim the draft genomes of Orthoptera. I like @gringers answer, it's a good one. As a project it would work. $\endgroup$
    – M__
    Commented Mar 17, 2023 at 21:28

1 Answer 1

2
$\begingroup$

It's possible that MOLE-BLAST could help for you:

MOLE-BLAST is an experimental tool that helps taxonomists find closest database neighbors of submitted query sequences. It computes a multiple sequence alignment (MSA) between the query sequences along with their top BLAST database hits, and generates a phylogenetic tree. Query sequences in the tree are denoted with highlighted node labels. If the input sequences come from different genes or loci, MOLE-BLAST can cluster them and compute an MSA and a phylogenetic tree for each locus separately. This tool may eventually be incorporated into our supported suite of BLAST applications based on the feedback we receive.

I haven't actually used MOLE-BLAST, but I have used Smart BLAST, which does a somewhat similar phylogenetic search (although on a restricted diverse taxonomic set) for protein queries.

$\endgroup$
1
  • $\begingroup$ thank you! I'll try that. $\endgroup$
    – Jacob
    Commented Mar 20, 2023 at 19:10

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.