20220502 DIAMOND homology searching on your PC

Seeking the protein in a sequence database that is the best match for a query sequence can take an hour via webserver, but you can often get much quicker results by performing the sequence alignment on your own computer! DIAMOND (github.com/bbu...) represents a very, very fast implementation of BLASTP that is currently freely available for both Windows and Linux computers. In this video, we walk through the example of finding orthologs for HugZ (www.uniprot.or...) in UniProt complete proteomes for six Helicobacter species (UP000000775, UP000001522, UP000002495, UP000007091, UP000007934, UP000008387). The commands required look like this:
diamond makedb --in uniprot-proteome_UP000002495-hepaticus.fasta -d hep
diamond.exe blastp -d hep -q HP0318.fasta
We briefly try to interpret the "Sequence Identity," "E-value," and "Bit Score" fields that the software returns along with sequence accessions.
At the conclusion of the video, we visualize a relatively weak homology using the European Bioinformatics Institute's WATER server (www.ebi.ac.uk/....

[@luispaterninatuiran6139]

Nice to watch a Diamond tutorial, it will be very helpful for us, thank you very much!

[@soura]

Absolutely amazing. Thankyou for explaining it beautifully!

[@myouiminari4524]

Thanks, very helpful

[@vishnuvijayan7891]

hello David...this was really useful...can i get your contact mail id ?

[@DavidTabb]

Hi, Vishnu. My current work email is dtabb on the server sun.ac.za. Thank you!