Ortholog assembly and extraction
I am extracting ortholog genes from genome databases, where genes are not annotated. I have used blast to generate hits against the database using genes of fully annotated genomes. Currently I am using Geneious to map these hits against the genes and then extract the assembled gene (which will have several gaps) Is there a way to automate this process of mapping the hits to the respective gene in one go?
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bagdiev39 •
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Many seem to use
orthofinderfor this purpose. See if it is useful: https://github.com/davidemms/OrthoFinderI really like
orthofinderand use it frequently, but there are also plenty of other tools out there. Here is a recent review with a few of the best tools and how they differ.