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TubercuList specifications

Information


Unique identifier OMICS_05811
Name TubercuList
Restrictions to use None
Maintained No

Taxon


  • Bacteria
    • Mycobacterium tuberculosis

Maintainer


This tool is not available anymore.

Publication for TubercuList

TubercuList citations

 (55)
library_books

A genome wide structure based survey of nucleotide binding proteins in M. tuberculosis

2017
Sci Rep
PMCID: 5624866
PMID: 28970579
DOI: 10.1038/s41598-017-12471-8

[…] illustrate the importance of the surveying at the level of binding site structures, we asked how many of these would be identified by a sequence search alone. A search for NTP binding proteins in the tuberculist database results in identifying 410 proteins, simply based on the known annotations. Using sequence motifs such as the Walker motif as the query, again a sequence-based search in PROSITE f […]

library_books

Delayed effects of transcriptional responses in Mycobacterium tuberculosis exposed to nitric oxide suggest other mechanisms involved in survival

2017
Sci Rep
PMCID: 5557973
PMID: 28811595
DOI: 10.1038/s41598-017-08306-1

[…] linear ion trap.Thermo raw files were converted into mzXML format using ProteoWizard. The acquired MS2 spectra were searched with OMSSA and XTandem against an M. tuberculosis H37Rv protein database (TubercuList v2.6) additionally containing reversed sequences of all proteins in the database. Search parameters were as follows: semi-tryptic peptides (proteolytic cleavage after lysine and arginine u […]

library_books

Mapping and characterization of G quadruplexes in Mycobacterium tuberculosis gene promoter regions

2017
Sci Rep
PMCID: 5515968
PMID: 28720801
DOI: 10.1038/s41598-017-05867-z

[…] ndidate genes”). This threshold was chosen according to Beaudoin et al., which did not validate G4s with lower score. These genes were classified according to their functional category as reported in TubercuList. In addition, a de novo function prediction based on Gene Ontology (GO) annotations was performed with the online server Argot2.5 to expand already available annotations and potentially de […]

library_books

Phenotypic and genomic comparison of Mycobacterium aurum and surrogate model species to Mycobacterium tuberculosis: implications for drug discovery

2017
BMC Genomics
PMCID: 5508667
PMID: 28705154
DOI: 10.1186/s12864-017-3924-y

[…] All functional categories were obtained using the Kyoto Encyclopedia of Genes and Genomes (KEGG) [] and Tuberculist (http://tuberculist.epfl.ch/). A python script was written to retrieve the Tuberculist and KEGG functional categories relative to M. tuberculosis H37Rv. Several python scripts were written […]

call_split

Whole transcriptomic and proteomic analyses of an isogenic M. tuberculosis clinical strain with a naturally occurring 15 Kb genomic deletion

2017
PLoS One
PMCID: 5484546
PMID: 28650996
DOI: 10.1371/journal.pone.0179996
call_split See protocol

[…] idered significant when they presented a fold change of ≥ 1.5 or ≤ -1.5 with a p-value < 0.01 when comparing the ON-A NM to ON-A WT. These genes were then categorized according to the function as per TubercuList (http://tuberculist.epfl.ch/). Raw data has been deposited in the NCBI database with accession numbers SRX2536569 and SRX2536568 for ON-A WT; and SRX2536567, SRX2536566 and SRX2536565 for […]

library_books

The EXIT Strategy: an Approach for Identifying Bacterial Proteins Exported during Host Infection

2017
MBio
PMCID: 5405230
PMID: 28442606
DOI: 10.1128/mBio.00333-17

[…] he homologous yeast O-mannosyltransferase (). It should be noted that our analysis did not identify any one prediction program as being better than others overall, including TMHMM () which is used on Tuberculist (); rather, it emphasized the value of the EXIT data to select the best model. For each of the 593 EXIT proteins, the site of enriched fusions to the reporter as well as all the in-frame E […]

Citations

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TubercuList institution(s)
Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Lausanne, Switzerland

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