Smart Blast searches a protein query against protein databases. SmartBLAST Tutorial
also another useful read on SmartBLAST
SmartBLAST is a new and experimental NCBI tool that makes it easier to complete common sequence analysis tasks, such as finding a candidate protein name for a sequence, locating regions of high sequence conservation, or identifying regions covered by database sequences but missing from the query.
BLAST (Basic Local Alignment Search Tool) is a popular tool for finding sequences in a given database that are similar to a query sequence. Traditionally, BLAST displays these results as a sorted list of matches between the query and each database sequence. While this display is useful for examining how each subject sequence matches the query, it treats all subject sequences the same, regardless of the quality of the sequence data or its annotation, and also does not allow easy comparisons between different subject sequences.
The Basic Local Alignment Search Tool (BLAST) 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.
Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. 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.
The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing.
The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. Protein sequences are the fundamental determinants of biological structure and function.
The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids
The Human Genome Project (HGP) was one of the great feats of exploration in history - an inward voyage of discovery rather than an outward exploration of the planet or the cosmos; an international research effort to sequence and map all of the genes - together known as the genome - of members of our species, Homo sapiens. Completed in April 2003, the HGP gave us the ability, for the first time, to read nature's complete genetic blueprint for building a human being.
The NCBI BioSystems Database provides integrated access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez.
The Protein Information Resource (PIR), located at Georgetown University Medical Center (GUMC), is an integrated public bioinformatics resource to support genomic and proteomic research.
Descriptions of new online databases covering various areas of molecular biology and papers describing recent updates to the databases previously described in NAR and other journals.
everyVECTOR is a revolutionary free molecular biology software platform designed and created by biologists. Collaborate: Share clearly annotated vector information. Discover: Organize all of your molecular biology information. Search through your own vectors by features such as promoters, genes, markers. Create: Design, create, and analyze new vectors using everyVECTOR's intuitive graphical editor and interface your data with a variety of online analysis tools. New user: http://www.everyvector.com/users/new Read: http://www.newyorker.com/magazine/2015/11/16/the-gene-hackers
Bioinformatics.ca through its Canadian Bioinformatics Workshops (CBW) series began offering one and two week short courses in bioinformatics, genomics and proteomics in 1999, in response to an identified need for a skilled bioinformatics workforce in Canada. In partnership with the Canadian Genetics Diseases Network and Human Resources Development Canada, and under the scientific direction of Director, Francis Ouellette, the CBW series was established. This initial series continued on for eight years.
AABME [from American Society of Mechanical Engineers (ASME)] is a new resource that brings together practitioners in the growing and increasingly indispensable discipline of biomedical engineering.
Tool for viewing molecular structures and data from multiple perspectives. Includes simultaneous views (3D graphics, sequences, data tables, etc.) plus functionality for simulating, building, editing, and analyzing structures. (Requires registration on the Accelrys website to download free software.)
Database of experimentally determined structures of proteins, DNA, and RNA from the Protein Data Bank (PDB). Includes chemical graphs, links to literature, similar sequences, related 3D structures, bound chemicals, and more. (Also known as Entrez Structure.)
Free program for displaying molecular structure of DNA, proteins, and smaller molecules. Can show molecules as wireframe bonds, space-filling spheres, macromolecular ribbons, dot surface representations, and more. Includes the ability to rotate, translate, zoom, etc.
Curated, annotated data about experimentally determined structures of proteins, nucleic acids, and complex assemblies. Includes tools for performing simple and advanced searches and visualizing, downloading, and analyzing the molecular structures.
Search service for identifying similarities between a selected protein structure and those in NCBI's MMDB/PDB database. Includes ability to browse list of structure neighbors and view superpositions and alignments.
