Bioinformatics Asked by 0x90 on December 9, 2020
I’d like to build the evolutionary history of a protein, given its sequence. Namely, given a FASTA entry how can I build an evolutionary tree? Here is the 5wxy protein as an example:
>5WXY:A|PDBID|CHAIN|SEQUENCE
MGHHHHHHMMKTKLPILGVLGGMGPVVTAEFLKSIYEYNPFIDKEQESPNVIVFSFPSAPDRTGSIDSGKEREFIDFIQV
NLEHLNKLADCIVIGSCTAHYALPQIPENLKDKLISLIKIADQELQEYNEPTLLLASTGTYQKKLFQEGCTTADLIISLS
ESDQKLIHEMIYKVLKRGHDPLSILRDIEALLEKYNTRSYISGSTEFHLLTKSLKLKGIDSIKAIDPLSTIAQNFSQLII
KQAQVDLVTDCHQPSNPKSP
Do I need to do some queries to Entrez in order to build the evolution tree?
I saw this paper, but I am not sure how I can use it with a single mammal’s protein primary sequence.
Question given a protein name, is it possible to look for its evolutionary history or build evolution tree using other databases beside PDB on top of bioinformatics algorithms.
The general procedure is:
Answered by Devon Ryan on December 9, 2020
There you go, its Microcystis aeruginosa aspartate/glutamate racemase. Easy does it. If you want to know how you can do this in 15 seconds let me know.
Its one of the new features of NCBI's Blast
Answered by Michael on December 9, 2020
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