TriTrypDB: An integrated functional genomics resource for kinetoplastida.
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 th...
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Online Access: | https://doi.org/10.1371/journal.pntd.0011058 https://doaj.org/article/376d108ca2a94805950a5651f8c3e5c9 |
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ftdoajarticles:oai:doaj.org/article:376d108ca2a94805950a5651f8c3e5c9 2023-05-15T15:08:27+02:00 TriTrypDB: An integrated functional genomics resource for kinetoplastida. Achchuthan Shanmugasundram David Starns Ulrike Böhme Beatrice Amos Paul A Wilkinson Omar S Harb Susanne Warrenfeltz Jessica C Kissinger Mary Ann McDowell David S Roos Kathryn Crouch Andrew R Jones 2023-01-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0011058 https://doaj.org/article/376d108ca2a94805950a5651f8c3e5c9 EN eng Public Library of Science (PLoS) https://doi.org/10.1371/journal.pntd.0011058 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0011058 https://doaj.org/article/376d108ca2a94805950a5651f8c3e5c9 PLoS Neglected Tropical Diseases, Vol 17, Iss 1, p e0011058 (2023) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2023 ftdoajarticles https://doi.org/10.1371/journal.pntd.0011058 2023-03-05T01:33:15Z 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. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLOS Neglected Tropical Diseases 17 1 e0011058 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
spellingShingle |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Achchuthan Shanmugasundram David Starns Ulrike Böhme Beatrice Amos Paul A Wilkinson Omar S Harb Susanne Warrenfeltz Jessica C Kissinger Mary Ann McDowell David S Roos Kathryn Crouch Andrew R Jones TriTrypDB: An integrated functional genomics resource for kinetoplastida. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Achchuthan Shanmugasundram David Starns Ulrike Böhme Beatrice Amos Paul A Wilkinson Omar S Harb Susanne Warrenfeltz Jessica C Kissinger Mary Ann McDowell David S Roos Kathryn Crouch Andrew R Jones |
author_facet |
Achchuthan Shanmugasundram David Starns Ulrike Böhme Beatrice Amos Paul A Wilkinson Omar S Harb Susanne Warrenfeltz Jessica C Kissinger Mary Ann McDowell David S Roos Kathryn Crouch Andrew R Jones |
author_sort |
Achchuthan Shanmugasundram |
title |
TriTrypDB: An integrated functional genomics resource for kinetoplastida. |
title_short |
TriTrypDB: An integrated functional genomics resource for kinetoplastida. |
title_full |
TriTrypDB: An integrated functional genomics resource for kinetoplastida. |
title_fullStr |
TriTrypDB: An integrated functional genomics resource for kinetoplastida. |
title_full_unstemmed |
TriTrypDB: An integrated functional genomics resource for kinetoplastida. |
title_sort |
tritrypdb: an integrated functional genomics resource for kinetoplastida. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2023 |
url |
https://doi.org/10.1371/journal.pntd.0011058 https://doaj.org/article/376d108ca2a94805950a5651f8c3e5c9 |
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Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 17, Iss 1, p e0011058 (2023) |
op_relation |
https://doi.org/10.1371/journal.pntd.0011058 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0011058 https://doaj.org/article/376d108ca2a94805950a5651f8c3e5c9 |
op_doi |
https://doi.org/10.1371/journal.pntd.0011058 |
container_title |
PLOS Neglected Tropical Diseases |
container_volume |
17 |
container_issue |
1 |
container_start_page |
e0011058 |
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1766339810053586944 |