TriTrypDB: an integrated functional genomics resource for kinetoplastida

Shanmugasundram, A. et al. (2023) TriTrypDB: an integrated functional genomics resource for kinetoplastida. PLoS Neglected Tropical Diseases, 17(1), e0011058. (doi: 10.1371/journal.pntd.0011058) (PMID:36656904) (PMCID:PMC9888696)

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Abstract

Parasitic diseases caused by kinetoplastid parasites are a burden to public health throughout tropical and subtropical regions of the world. TriTrypDB (https://tritrypdb.org) is a free online resource for data mining of genomic and functional data from these kinetoplastid parasites and is part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org). As of release 59, TriTrypDB hosts 83 kinetoplastid genomes, nine of which, including Trypanosoma brucei brucei TREU927, Trypanosoma cruzi CL Brener and Leishmania major Friedlin, undergo manual curation by integrating information from scientific publications, high-throughput assays and user submitted comments. TriTrypDB also integrates transcriptomic, proteomic, epigenomic, population-level and isolate data, functional information from genome-wide RNAi knock-down and fluorescent tagging, and results from automated bioinformatics analysis pipelines. TriTrypDB offers a user-friendly web interface embedded with a genome browser, search strategy system and bioinformatics tools to support custom in silico experiments that leverage integrated data. A Galaxy workspace enables users to analyze their private data (e.g., RNA-sequencing, variant calling, etc.) and explore their results privately in the context of publicly available information in the database. The recent addition of an annotation platform based on Apollo enables users to provide both functional and structural changes that will appear as ‘community annotations’ immediately and, pending curatorial review, will be integrated into the official genome annotation.

Item Type:Articles
Additional Information:Funding: This work was supported by the National Institute of Allergy and Infectious Diseases (NIAID, https://www.niaid.nih.gov/) — National Institutes of Health (NIH) Contract #75N93019C00077 to DSR, MAM & JCK and Wellcome Trust (https:// wellcome.org) grants 218288/Z/19/Z and 212929/ Z/18/Z to ARJ, KC, DSR & JCK.
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Crouch, Dr Kathryn
Creator Roles:
Crouch, K.Conceptualization, Funding acquisition, Project administration, Writing – review and editing
Authors: Shanmugasundram, A., Starns, D., Böhme, U., Amos, B., Wilkinson, P. A., Harb, O. S., Warrenfeltz, S., Kissinger, J. C., McDowell, M. A., Roos, D. S., Crouch, K., and Jones, A. R.
College/School:College of Medical Veterinary and Life Sciences > School of Infection & Immunity
Journal Name:PLoS Neglected Tropical Diseases
Publisher:Public Library of Science
ISSN:1935-2727
ISSN (Online):1935-2735
Published Online:19 January 2023
Copyright Holders:Copyright © 2023 Shanmugasundram et al.
First Published:First published in PLoS Neglected Tropical Diseases 17(1): e0011058
Publisher Policy:Reproduced under a Creative Commons license

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