EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2022

Thakur, Matthew; Bateman, Alex; Brooksbank, Cath; Freeberg, Mallory; Harrison, Melissa; Hartley, Matthew; Keane, Thomas M.; Kleywegt, Gerard J.; Leach, Andrew R.; Levchenko, Maria; Morgan, Sarah; McDonagh, Ellen M.; Orchard, Sandra; Papatheodorou, Irene; Velankar, Sameer; Vizcaíno, Juan Antonio; Witham, Rick; Zdrazil, Barbara; McEntyre, Johanna

doi:10.1093/nar/gkac1098

Cited by 30 publications

(15 citation statements)

References 60 publications

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“…Regarding the annotation file, two formats are acceptable: (i) generic feature format files (GFF) and (ii) protein/RNA table files (PTT/RNT). These files can be easily obtained from a variety of publicly available databases such as NCBI [44], EMBL [45], DDBJ [46], etc. In the case of a newly sequenced organism, they can also be generated using genome annotation pipeline like PGAP [47].…”

Section: Methodsmentioning

confidence: 99%

GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes

Xiang

Feng

Xing

et al. 2022

Preprint

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Pooled CRISPRi with high-throughput sequencing is emerging as a novel functional genomic study method in prokaryotes. Due to the diversity of sgRNA activity and off-target effect, it is crucial to have a robust sgRNA library designing tool. Here we propose a web tool named CRISPRi-FGP (http://www.thu-big.net/sgRNA_design/), to assist sgRNA library design in prokaryotes. CRISPRi-FGP applies a build-in database containing 1,300 common prokaryotes as standard designing source, while also accepts customized designing. It employs a scoring metrics based on experiment data, together with specially trimed algorithm for off-target selection both in high quality and speed. CRISPRi-FGP exhibited high accuracy and robustness on sgRNA library designing in multiple prokaryotes. Finally, an experiment comparing CRISPRi-FGP and existing tool was conducted and showed CRISPRi-FGP has improved ability in recognizing off-target sites. All these results showed CRISPRi-FGP with the potential to be a precise and robust tool for high-quality sgRNA library design in prokaryotes.

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Section: Methodsmentioning

confidence: 99%

GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes

Xiang

Feng

Xing

et al. 2022

Preprint

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“…Regarding the annotation le, two formats are acceptable: (i) generic feature format les (GFF) and (ii) protein/RNA table les (PTT/RNT). These les can be easily obtained from a variety of publicly available databases such as NCBI [28], EMBL [29], DDBJ [30], etc. In the case of a newly sequenced organism, they can also be generated using genome annotation pipeline like PGAP [31].…”

Section: Data Prerequisites For the Design Of Sgrna Librarymentioning

confidence: 99%

GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes

Xiang,

Feng,

Xing

et al. 2024

Preprint

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Background CRISPRi screening has become a powerful approach for functional genomic research. However, the off-target effects resulting from the mismatch tolerance between sgRNAs and their intended targets is a primary concern in CRISPRi applications. Results We introduce Guide Library Designer (GLiDe), a web-based tool specifically created for the genome-scale design of sgRNA libraries tailored for CRISPRi screening in prokaryotic organisms. GLiDe incorporates a robust quality control framework, rooted in prior experimental knowledge, ensuring the accurate identification of off-target hits. It boasts an extensive built-in database, encompassing 1,397 common prokaryotic species as a comprehensive design resource. Conclusions GLiDe provides the capability to design sgRNAs for newly discovered organisms. We further demonstrated that GLiDe exhibits enhanced precision in identifying off-target binding sites for the CRISPRi system.

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“…Finally, six databases most recently published elsewhere contribute updates (Table 2 ). As usual, updates from the major database providers at the European Bioinformatics Institute (EBI), the U.S. National Center for Biotechnology Information (NCBI), and the National Genomics Data Center (NGDC) in China ( 1–3 ) are placed first. The usual categorisation then follows: (i) nucleic acid sequence and structure, transcriptional regulation; (ii) protein sequence and structure; (iii) metabolic and signalling pathways, enzymes and networks; (iv) genomics of viruses, bacteria, protozoa and fungi; (v) genomics of human and model organisms plus comparative genomics; (vi) human genomic variation, diseases and drugs; (vii) plants and (viii) other topics, such as proteomics databases.…”

Section: New and Updated Databasesmentioning

confidence: 99%

The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection

Rigden

Fernández

2023

Nucleic Acids Research

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The 2023 Nucleic Acids Research Database Issue contains 178 papers ranging across biology and related fields. There are 90 papers reporting on new databases and 82 updates from resources previously published in the Issue. Six more papers are updates from databases most recently published elsewhere. Major nucleic acid databases reporting updates include Genbank, ENA, ChIPBase, JASPAR, mirDIP and the Issue's first Breakthrough Article, NACDDB for Circular Dichroism data. Updates from BMRB and RCSB cover experimental protein structural data while AlphaFold 2 computational structure predictions feature widely. STRING and REBASE are stand-out updates in the signalling and enzymes section. Immunology-related databases include CEDAR, the second Breakthrough Article, for cancer epitopes and receptors alongside returning IPD-IMGT/HLA and the new PGG.MHC. Genomics-related resources include Ensembl, GWAS Central and UCSC Genome Browser. Major returning databases for drugs and their targets include Open Targets, DrugCentral, CTD and Pubchem. The EMPIAR image archive appears in the Issue for the first time. The entire database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been updated, revisiting 463 entries, adding 92 new resources and eliminating 96 discontinued URLs so bringing the current total to 1764 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.

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EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2022

Cited by 30 publications

References 60 publications

GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes

GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes

GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes

The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection

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