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Mycobrowser specifications

Information


Unique identifier OMICS_28542
Name Mycobrowser
Alternative name Mycobacterial browser
Restrictions to use None
Database management system PostgreSQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Bacteria
    • Mycobacterium tuberculosis

Maintainers


  • person_outline Stewart Cole
  • person_outline Adamandia Kapopoulou
  • person_outline Jocelyne Lew

Publication for Mycobacterial browser

Mycobrowser citations

 (7)
library_books

Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans

2018
Nat Commun
PMCID: 5931558
PMID: 29717136
DOI: 10.1038/s41467-018-03857-x

[…] and downstream SNPs located further than 100 bases away from a gene were ignored. The annotations were manually completed with information about transcript type and function available on the NCBI and Mycobrowser databases. The results were compiled into a table containing information for each SNP regarding its effect on the genes in the strains in which the SNP occurs (Supplementary Data ). In viv […]

library_books

HadD, a novel fatty acid synthase type II protein, is essential for alpha and epoxy mycolic acid biosynthesis and mycobacterial fitness

2018
Sci Rep
PMCID: 5902629
PMID: 29662082
DOI: 10.1038/s41598-018-24380-5

[…] Analyses of genome sequences were done via the SmegmalList (http://mycobrowser.epfl.ch/smegmalist.html) and the NCBI (www.ncbi.nlm.nih.gov/genomes/lproks.cgi) web sites. Sequence alignments were performed using BLAST and Clustal Omega softwares,, with default paramet […]

library_books

Mycobacterial DNA binding protein 1 is critical for long term survival of Mycobacterium smegmatis and simultaneously coordinates cellular functions

2017
Sci Rep
PMCID: 5533761
PMID: 28754952
DOI: 10.1038/s41598-017-06480-w

[…] The false discovery rate against the decoy database was <1%. Gene Ontology annotation including protein molecular function and biological processes were searched using the SmegmaList database (http://mycobrowser.epfl.ch/smegmalist.html) and UniProt database (http://www.uniprot.org/). […]

library_books

Rational engineering of a virulence gene from Mycobacterium tuberculosis facilitates proteomic analysis of a natural protein N terminus

2016
Sci Rep
PMCID: 5021934
PMID: 27625110
DOI: 10.1038/srep33265

[…] to right). Peptide lengths were determined and used to create a heat map using the open source programming software, R. For analysis of the Esx-like proteins in , protein sequences were obtained from Mycobrowser and were analyzed in silico for digestion by trypsin with PeptideCutter (ExPASy). Protein graphics were generated using Microsoft Excel. […]

library_books

MycoBASE: expanding the functional annotation coverage of mycobacterial genomes

2015
BMC Genomics
PMCID: 4690229
PMID: 26704706
DOI: 10.1186/s12864-015-2311-9

[…] attempt to fill this gap was made by GenoMycDB [], a collection of six mycobacterial genomes; however, this database has not been updated to include more genomes. TubercuList was later extended into MycoBrowser []. This website contains a comprehensive genomic and proteomic database for three additional mycobacterial species; although, it still lacks commonly studied NTM such as M. avium complex […]

library_books

Genome analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of the etiologic agent of tuberculosis

2013
Nat Genet
PMCID: 3856870
PMID: 23291586
DOI: 10.1038/ng.2517

[…] risons were performed with the Microscope platform, Artemis and Artemis comparison tool (ACT). When applicable, annotations were transferred from those of M. tuberculosis orthologs in the TubercuList/Mycobrowser database, using BLAST matches of > 90% protein sequence identity, an alignable region of > 80% of the shortest protein length in pairwise comparisons and visual inspection of the gene synt […]

Citations

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Mycobrowser institution(s)
Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
Mycobrowser funding source(s)
Supported by the TB Drug Accelerator program, part of the Bill and Melinda Gates Foundation (grant no. 42917_BMGF).

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