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Open AccessJournal ArticleDOI

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022.

TLDR
The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and industry.
Abstract
The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and industry. With the explosively accumulated multi-omics data at ever-faster rates, CNCB-NGDC is constantly scaling up and updating its core database resources through big data archive, curation, integration and analysis. In the past year, efforts have been made to synthesize the growing data and knowledge, particularly in single-cell omics and precision medicine research, and a series of resources have been newly developed, updated and enhanced. Moreover, CNCB-NGDC has continued to daily update SARS-CoV-2 genome sequences, variants, haplotypes and literature. Particularly, OpenLB, an open library of bioscience, has been established by providing easy and open access to a substantial number of abstract texts from PubMed, bioRxiv and medRxiv. In addition, Database Commons is significantly updated by cataloguing a full list of global databases, and BLAST tools are newly deployed to provide online sequence search services. All these resources along with their services are publicly accessible at https://ngdc.cncb.ac.cn.

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KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences

TL;DR: KaKs_Calculator 3.0 as mentioned in this paper is an updated toolkit that is capable of calculating selective pressure on both coding and non-coding sequences, similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences.
Journal ArticleDOI

The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains

TL;DR: Wang et al. as mentioned in this paper found that weak effector-trigger immunity (ETI)-mediated primarily by Pi genes but not PTI results in the universal susceptibility of Lijiangxintuanheigu to rice blast.
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Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing

TL;DR: In this article , a collection of 171 full-length single-cell RNA-seq datasets is presented to explore the cellular landscape of circRNAs in human and mouse tissues, and the authors identify a total of 139,643 human and 214,747 mouse circRNA in these scRNA-seq libraries.
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LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations

TL;DR: Li et al. as mentioned in this paper presented LncBook 2.0 (https://ngdc.cncb.ac.cn/lncbook), which incorporated 119 722 new transcripts, 9632 new genes, and gene structure update of 21 305 lncRNAs.
References
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Journal ArticleDOI

Basic Local Alignment Search Tool

TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
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The EMBL-EBI search and sequence analysis tools APIs in 2019

TL;DR: The latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility, interoperability and reusability are described.
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A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.

TL;DR: A rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread and is designed to provide a real-time bird’s-eye view of the diversity of the hundreds of thousands of genome sequences collected worldwide.