A software program enabling sets of DNA of microorganisms living in different environments to be quickly compared...
Originally shared by Wayne Radinsky
A software program enabling sets of DNA of microorganisms living in different environments to be quickly compared has been developed. The program is called MetaFast (because the genomes of all the organisms living on another organism are called the "metagenome") and works by representing the shotgun metagenome as a modified de Bruijn graph consisting of simplified components, which can be used to obtain a pairwise similarity matrix. This similarity matrix indicates the subspecies-level diversity of the microbiota. The technique is expected to be used for personalized medicine tailored to the bacteria that live in and on people.
Source code is at
https://github.com/ctlab/metafast
http://en.ifmo.ru/en/viewnews/5732/Personalized_Medicine_to_Employ_Computer_Algorithms.htm
A software program enabling sets of DNA of microorganisms living in different environments to be quickly compared has been developed. The program is called MetaFast (because the genomes of all the organisms living on another organism are called the "metagenome") and works by representing the shotgun metagenome as a modified de Bruijn graph consisting of simplified components, which can be used to obtain a pairwise similarity matrix. This similarity matrix indicates the subspecies-level diversity of the microbiota. The technique is expected to be used for personalized medicine tailored to the bacteria that live in and on people.
Source code is at
https://github.com/ctlab/metafast
http://en.ifmo.ru/en/viewnews/5732/Personalized_Medicine_to_Employ_Computer_Algorithms.htm
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