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The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence Database Collaboration (INSDC).
T-Coffee is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences alignments obtained previously and in the latest versions can use structural information from PDB files (3D-Coffee). It has advanced features to evaluate the quality of the alignments and some capacity for identifying occurrence of motifs (Mocca). It produces alignment in the aln format (Clustal) by default, but can also produce PIR, MSF, and FASTA format. The most common input formats are supported.
David J. Lipman is an American biologist who from 1989 to 2017 was the director of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. NCBI is the home of GenBank, the U.S. node of the International Sequence Database Consortium, and PubMed, one of the most heavily used sites in the world for the search and retrieval of biomedical information. Lipman is one of the original authors of the BLAST sequence alignment program, and a respected figure in bioinformatics. In 2017, he left NCBI and became Chief Science Officer at Impossible Foods.
The Pathogen-Host Interactions database (PHI-base) is a biological database that contains manually curated information on genes experimentally proven to affect the outcome of pathogen-host interactions. The database has been maintained by researchers at Rothamsted Research and external collaborators since 2005. PHI-base has been part of the UK node of ELIXIR, the European life-science infrastructure for biological information, since 2016.
The Integrated Microbial Genomes system is a genome browsing and annotation platform developed by the U.S. Department of Energy (DOE)-Joint Genome Institute. IMG contains all the draft and complete microbial genomes sequenced by the DOE-JGI integrated with other publicly available genomes. IMG provides users a set of tools for comparative analysis of microbial genomes along three dimensions: genes, genomes and functions. Users can select and transfer them in the comparative analysis carts based upon a variety of criteria. IMG also includes a genome annotation pipeline that integrates information from several tools, including KEGG, Pfam, InterPro, and the Gene Ontology, among others. Users can also type or upload their own gene annotations and the IMG system will allow them to generate Genbank or EMBL format files containing these annotations.
Mouse Genome Informatics (MGI) is a free, online database and bioinformatics resource hosted by The Jackson Laboratory, with funding by the National Human Genome Research Institute (NHGRI), the National Cancer Institute (NCI), and the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). MGI provides access to data on the genetics, genomics and biology of the laboratory mouse to facilitate the study of human health and disease. The database integrates multiple projects, with the two largest contributions coming from the Mouse Genome Database and Mouse Gene Expression Database (GXD). As of 2018, MGI contains data curated from over 230,000 publications.
In molecular biology, STRING is a biological database and web resource of known and predicted protein–protein interactions.
Pathogenomics is a field which uses high-throughput screening technology and bioinformatics to study encoded microbe resistance, as well as virulence factors (VFs), which enable a microorganism to infect a host and possibly cause disease. This includes studying genomes of pathogens which cannot be cultured outside of a host. In the past, researchers and medical professionals found it difficult to study and understand pathogenic traits of infectious organisms. With newer technology, pathogen genomes can be identified and sequenced in a much shorter time and at a lower cost, thus improving the ability to diagnose, treat, and even predict and prevent pathogenic infections and disease. It has also allowed researchers to better understand genome evolution events - gene loss, gain, duplication, rearrangement - and how those events impact pathogen resistance and ability to cause disease. This influx of information has created a need for bioinformatics tools and databases to analyze and make the vast amounts of data accessible to researchers, and it has raised ethical questions about the wisdom of reconstructing previously extinct and deadly pathogens in order to better understand virulence.
Therapeutic Target Database (TTD) is a pharmaceutical and medical repository constructed by the Innovative Drug Research and Bioinformatics Group (IDRB) at Zhejiang University, China and the Bioinformatics and Drug Design Group at the National University of Singapore. It provides information about known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Detailed knowledge about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, and clinical development status. TTD is freely accessible without any login requirement at https://idrblab.org/ttd/.
Bacterial small RNAs are small RNAs produced by bacteria; they are 50- to 500-nucleotide non-coding RNA molecules, highly structured and containing several stem-loops. Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as Northern blotting, microarrays and RNA-Seq in a number of bacterial species including Escherichia coli, the model pathogen Salmonella, the nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti, marine cyanobacteria, Francisella tularensis, Streptococcus pyogenes, the pathogen Staphylococcus aureus, and the plant pathogen Xanthomonas oryzae pathovar oryzae. Bacterial sRNAs affect how genes are expressed within bacterial cells via interaction with mRNA or protein, and thus can affect a variety of bacterial functions like metabolism, virulence, environmental stress response, and structure.
OMPdb is a dedicated database that contains beta barrel (β-barrel) outer membrane proteins from Gram-negative bacteria. Such proteins are responsible for a broad range of important functions, like passive nutrient uptake, active transport of large molecules, protein secretion, as well as adhesion to host cells, through which bacteria expose their virulence activity.
The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of sequence assembly and other metadata related to sequencing projects. The archive is composed of three main databases: the Sequence Read Archive, the Trace Archive and the EMBL Nucleotide Sequence Database. The ENA is produced and maintained by the European Bioinformatics Institute and is a member of the International Nucleotide Sequence Database Collaboration (INSDC) along with the DNA Data Bank of Japan and GenBank.
Mycoplasma penetrans is a species of Gram-positive bacteria. It is pathogenic, though many infected show no symptoms. It is a sexually transmitted disease, though an infant may be infected during birth.
Donna R. Maglott is a staff scientist at the National Center for Biotechnology Information known for her research on large-scale genomics projects, including the mouse genome and development of databases required for genomics research.
Bacterial phylodynamics is the study of immunology, epidemiology, and phylogenetics of bacterial pathogens to better understand the evolutionary role of these pathogens. Phylodynamic analysis includes analyzing genetic diversity, natural selection, and population dynamics of infectious disease pathogen phylogenies during pandemics and studying intra-host evolution of viruses. Phylodynamics combines the study of phylogenetic analysis, ecological, and evolutionary processes to better understand of the mechanisms that drive spatiotemporal incidence and phylogenetic patterns of bacterial pathogens. Bacterial phylodynamics uses genome-wide single-nucleotide polymorphisms (SNP) in order to better understand the evolutionary mechanism of bacterial pathogens. Many phylodynamic studies have been performed on viruses, specifically RNA viruses which have high mutation rates. The field of bacterial phylodynamics has increased substantially due to the advancement of next-generation sequencing and the amount of data available.
In molecular biology, MvirDB was a publicly available database that stored information on toxins, virulence factors and antibiotic resistance genes. Sources that this database used for DNA and protein information included: Tox-Prot, SCORPION, the PRINTS Virulence Factors, VFDB, TVFac, Islander, ARGO and VIDA. The database provided a BLAST tool that allowed the user to query their sequence against all DNA and protein sequences in MvirDB. Information on virulence factors could be obtained from the usage of the provided browser tool. Once the browser tool was used, the results were returned as a readable table that was organized by ascending E-Values, each of which were hyperlinked to their related page. MvirDB was implemented in an Oracle 10g relational database. MvirDB appears to have been inactive for some time, and is therefore not current. The last available snapshot was made on August 2, 2017.
Ivan Erill is a Spanish computational biologist known for his research in comparative genomics and molecular microbiology. His work focuses primarily on bacterial comparative genomics, through the development of computational methods for analyzing regulatory networks and their evolution.
HOCOMOCO is an open-access database providing curated and benchmarked binding motifs of human and mouse transcription factors. It captures the following data types: Homo sapiens (human) and Mus musculus (mouse) transcription factors, their DNA binding site motifs, and motif subtypes.
References
- 1 2 3 Chen, L. (2004-12-17). "VFDB: a reference database for bacterial virulence factors". Nucleic Acids Research. 33 (Database issue): D325–D328. doi:10.1093/nar/gki008. ISSN 1362-4962. PMC 539962 . PMID 15608208.
- ↑ Altschul, S. (1997-09-01). "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs". Nucleic Acids Research. 25 (17): 3389–3402. doi:10.1093/nar/25.17.3389. ISSN 1362-4962. PMC 146917 . PMID 9254694.
- ↑ Benson, D. A.; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Sayers, E. W. (2009-01-01). "GenBank". Nucleic Acids Research. 37 (Database): D26–D31. doi:10.1093/nar/gkn723. ISSN 0305-1048. PMC 2686462 . PMID 18940867.
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