I'm an informatics student who has essentially zero knowledge of biology. I BLASTed my gene and have 1000s of results with very low E values. Where do I go from here if I want to find orthologues?
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1$\begingroup$ Please edit your question and give us some more details. What type of blast? Blastn? Tblastn? Blastx? Something else? Is your database protein or nucleotide? And your query? What species are you working with? What kind of orthologs do you want? (see here for a short discussion of orthologs vs paralogs; I suspect you just want general homologs). $\endgroup$– terdon ♦Nov 21, 2018 at 17:28
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3 Answers
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BLAST is often a sensible way to find gene/protein homologs, but resolving those as orthologs vs paralogs etc. is a non-trivial task, especially when considering large numbers of species.
Since you are new to bioinformatics I recommend you search an ortholog database that already exists.
Here are some databases:
All of these should allow you to search either with text or a sequence to identify the orthologous groups that your input belongs to at different taxonomic levels. Sequence searches either follow pairwise alignment (e.g. BLAST, DIAMOND, RAPSEARCH) or profile HMM type (e.g. HMMER3) approaches.
A more complete list of ortholog databases is available from "Quest for orthologs".
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Two solutions based around the same premise:
Repeat the blast using "blastp". I suspect you have used blastn (nucleotides). To translate the gene Expasy is okay and find the common "translate", here.
Blasted via Blastx without any modification to the gene.
Blast is capable of doing just about anything if you are aware of all its parameters.
The reasoning is that the gene you have will be under-represented in the database. By switching to amino acids there is a much greater chance of finding orthologous hits.
