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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!

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    $\begingroup$ Are these annotated, known genes? Or do you also need to detect/identify the potential homologs in the target species? $\endgroup$
    – terdon ♦
    Mar 16 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__ ♦
    Mar 17 at 21:28

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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.

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

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