Department: Computer Science & Engineering
Research Institute Affiliation: Center for Microbiome Innovation
Faculty Advisor(s): Rob Knight

Primary Student
Name: James Morton
Email: jmorton@eng.ucsd.edu
Phone: 858-534-0007
Grad Year: 2017

Student Collaborators
Zech Xu, zhenjiang.xu@gmail.com

With plunging cost of high-throughput sequencing, enormous amount of microbial genomic and metagenomic sequences are deposited into databases. The interpretation of these sequences requires consistent and high-quality annotation, which has been proven to be a major challenge in maintaining publically available databases such as Genbank. Here we have implemented a full, open-source annotation pipeline for bacterial and archaeal genomes, micronota. It wraps on the state-of-the-art tools to predict DNA features including coding genes, ncRNAs, CRISPR, prophage, and more. To provide consistent annotation across microbial genomes, micronota interfaces with multiple databases such as UniRef, UniProt, TIGRFam and PFam. Furthermore, micronota is actively developed and maintained with scalability and customizability in mind, which allows users to customize the individual tools and databases and annotate microbial genomes in their own laptop.

Industry Application Area(s)
Life Sciences/Medical Devices & Instruments | Software, Analytics

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Contact:   researchexpo@soe.ucsd.edu   (858) 534-6068