Biological Databases/resources
- PubMed
PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. It comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites
- UniProtKB
Provide the scientific community with a comprehensive, high-quality ad freely accessible resource of protein sequence, as well as functional information
- NCBI
The National Center for Biotechnology Information (NCBI) advances science and health by providing access to biomedical and genomic information
- GenBank
GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration , which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis.
A GenBank release occurs every two months and is available from the ftp site. The release notes for the current version of GenBank provide detailed information about the release and notifications of upcoming changes to GenBank. Release notes for previous GenBank releases are also available. GenBank growth statistics for both the traditional GenBank divisions and the WGS division are available from each release. GenBank growth statistics for both the traditional GenBank divisions and the WGS division are available from each release.
- Ensembl
The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online
- InterPro
InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as signatures, provided by several different databases (referred to as member databases) that make up the InterPro consortium
- OMIM
A comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily. OMIM is authored and edited at the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, under the direction of Dr. Ada Hamosh. Its official home is omim.org
- RCSB PDB (The Research Collaboratory for Structural Bioinformatics Protein Data Bank)
A member of the wwPDB, the RCSB PDB curates and annotates PDB data protein
structures. The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond.
- KEGG (Kyoto Encyclopedia of Genes and Genomes)
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. It comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites
Provide the scientific community with a comprehensive, high-quality ad freely accessible resource of protein sequence, as well as functional information
The National Center for Biotechnology Information (NCBI) advances science and health by providing access to biomedical and genomic information
GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration , which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis.
A GenBank release occurs every two months and is available from the ftp site. The release notes for the current version of GenBank provide detailed information about the release and notifications of upcoming changes to GenBank. Release notes for previous GenBank releases are also available. GenBank growth statistics for both the traditional GenBank divisions and the WGS division are available from each release. GenBank growth statistics for both the traditional GenBank divisions and the WGS division are available from each release.
The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online
InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as signatures, provided by several different databases (referred to as member databases) that make up the InterPro consortium
A comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily. OMIM is authored and edited at the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, under the direction of Dr. Ada Hamosh. Its official home is omim.org
A member of the wwPDB, the RCSB PDB curates and annotates PDB data protein structures. The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond.
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
Web-tools/tools
- UbiSite: A web server for identifying protein ubiquitination sites
- UbiNet: A web resource for exploring Ubiquitination networks
- dbPTM: An Integrated Resource for Protein Post-Translational Modifications
- dbSNO: A database of Cysteine S-nitrosylation
- RegPhos: A resource to explore the protein kinase-substrate phosphorylation networks in human and mouse
- PlantPhos: a web tool for predicting potential phosphorylation sites in plant proteins
- ViralPhos: a web server for identifying potential virus phosphorylation sites with substrate motifs.
- SNOsite: An effective web-based tool for identifying S-NitrOsylation Site on cysteine
- MDDLogo: New approach that applies maximal dependence decomposition (MDD) to cluster a group of aligned signal sequences into subgroups, which have statistically significant motifs
- CD-HIT A very widely used program for clustering and comparing protein or nucleotide sequences.
CD-HIT is very fast and can handle extremely large databases. It helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. - BLAST (Basic Local Alignment Search Tool - NCBI) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families
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