Dataset Information

Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families.

ABSTRACT: Capturing the published corpus of information on all members of a given protein family should be an essential step in any study focusing on specific members of that family. Using a previously gathered dataset of more than 280 references mentioning a member of the DUF34 (NIF3/Ngg1-interacting Factor 3) family, we evaluated the efficiency of different databases and search tools, and devised a workflow that experimentalists can use to capture the most information published on members of a protein family in the least amount of time. To complement this workflow, web-based platforms allowing for the exploration of protein family members across sequenced genomes or for the analysis of gene neighbourhood information were reviewed for their versatility and ease of use. Recommendations that can be used for experimentalist users, as well as educators, are provided and integrated within a customized, publicly accessible Wiki.

SUBMITTER: Reed CJ

PROVIDER: S-EPMC10926702 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

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Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families.

Reed Colbie J CJ Denise Rémi R Hourihan Jacob J Babor Jill J Jaroch Marshall M Martinelli Maria M Hutinet Geoffrey G de Crécy-Lagard Valérie V

Microbial genomics 20240201 2

Capturing the published corpus of information on all members of a given protein family should be an essential step in any study focusing on specific members of that family. Using a previously gathered dataset of more than 280 references mentioning a member of the DUF34 (NIF3/Ngg1-interacting Factor 3) family, we evaluated the efficiency of different databases and search tools, and devised a workflow that experimentalists can use to capture the most information published on members of a protein f ...[more]

PMID: 38323604

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Project description:BackgroundOrenburg Region is located in the South Urals, mostly in the steppe zone and is characterised by various landscapes suitable for many Chenopodiaceae. The species of Chenopodiaceae are present in all major plant communities (saline vegetation, steppes, on limestone, chalk and sand, and as degraded or ruderal communities). In the steppe zone, many native subshrubby species (Atriplexcana, Caroxylonlaricinum, Suaedaphysophora) playing a crucial role in semi-deserts (known as southern steppes in the recent Russian literature) located southwards of Orenburg Region are locally found, and several annuals (Salicorniaperennans, Suaeda spp.) are most common dominants in plant communities. Some typical semi-desert species (Kalidiumfoliatum, Bassiahyssopifolia, Sodafoliosa, Spirobassiahirsuta) are found in the easternmost part of the region.New informationWe compiled a checklist of Chenopodiaceae in Orenburg Region, with two new records (Chenopodiumvirgatum, Corispermumlaxiflorum), based on our critical revision, comprehensive inventory of herbarium specimens and documented observations and field research. In total, we report 76 species in the Region, which is the third-highest number of the Chenopodiaceae species compared with other administrative territories of European Russia, North Caucasus and West Siberia. Alien and native taxa are distinguished. Zonal patterns of species distributions are confirmed. A preliminary conservation status is proposed for each native species. Three species are recommended for exclusion from the Red Data Book of Orenburg Region: Petrosimoniatriandra (because of its extensive distribution), Kalidiumfoliatum and Anabasissalsa (because of the lack of actual threat to their populations). Arthrophytumlehmannianum and Salsolarosacea are considered threatened (Vulnerable) because of their restricted occurrence and population size and because their localities are under anthropogenic pressure. Atriplexhortensis, Atriplexrosea, Chenopodiumacuminatum, C.karoi, C.praetericola, C.vulvaria, Climacopteraaffinis, C.crassa, Halimocnemiskarelinii, Salsolapaulsenii and Xylosalsolaarbuscula are excluded from the checklist, based on various reasons as discussed in the paper. Point distribution maps are provided for each species. Agriophyllumpungens (Vahl) Link is accepted as the correct authorship instead of "M.Bieb. ex C.A.Mey."

Dataset Information

Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families.

Publications

Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families.

Similar Datasets

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