20220502 DIAMOND homology searching on your PC
Автор: David Tabb
Загружено: 2022-05-02
Просмотров: 1989
Описание:
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 (https://github.com/bbuchfink/diamond) 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 (https://www.uniprot.org/uniprot/O2508...) 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 (https://www.ebi.ac.uk/Tools/psa/embos....
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