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SEA-PHAGES
SEA-PHAGES stands for Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science; it was formerly called the National Genomics Research Initiative. This was the first initiative launched by the Howard Hughes Medical Institute (HHMI) Science Education Alliance (SEA) by their director Tuajuanda C. Jordan in 2008 to improve the retention of Science, technology, engineering, and mathematics (STEM) students. SEA-PHAGES is a two-semester undergraduate research program administered by the University of Pittsburgh's Graham Hatfull's group and the Howard Hughes Medical Institute's Science Education Division. Students from over 100 universities nationwide engage in authentic individual research that includes a wet-bench laboratory and a bioinformatics component. Curriculum During the first semester of this program, classes of around 18-24 undergraduate students work under the supervision of one or two university faculty members and a graduate student assistant� ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Graham Hatfull
Graham F. Hatfull is the Eberly Family Professor of Biotechnology at the University of Pittsburgh, where he studies bacteriophages. He has been an HHMI professor since 2002, and is the creator of their SEA-PHAGES program. Life and career Hatfull studied biological sciences at Westfield College, University of London from 1975 to 1978. He received his PhD from the University of Edinburgh in 1981. He did postdoctoral research at Yale University and the Medical Research Council. In 2002, he developed the SEA-PHAGES, originally the PHIRE (Phage Hunters Integrating Research and Education) program, which he originally developed to include 10-12 students per year. The program existed only at the University of Pittsburgh from 2002 to 2008, when the HHMI created the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program. The first year of SEA-PHAGES, the program had 12 participative universities. The program has since spread to more t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PhagesDB
The Actinobacteriophage database, more commonly known as PhagesDB, is a website and database that gathers and shares information related to the discovery, characterization and genomics of viruses that prefer to infect Actinobacterial hosts. It is used to compare phages and their genomic annotations. The database provides information on more than 8,000 bacteriophages, including over 1,600 with already sequenced genomes. Background PhagesDB provides the Actinobacteriophage research community with a database to post findings for analysis and further research. Design and features The creation of PhagesDB was carried out using Django and was hosted on a WebFaction server. The database website opens up with a mostly green and black lobby page and on the top left, a search bar is present. Phage names can be, sequenced and/or draft, typed in the search bar and results immediately pop up. PhagesDB has individual pages for every phage in the database. Along with all these, there is a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Howard Hughes Medical Institute
The Howard Hughes Medical Institute (HHMI) is an American non-profit medical research organization based in Chevy Chase, Maryland. It was founded in 1953 by Howard Hughes, an American business magnate, investor, record-setting pilot, engineer, film director, and philanthropist, known during his lifetime as one of the most financially successful individuals in the world. It is one of the largest private funding organizations for biological and medical research in the United States. HHMI spends about $1 million per HHMI Investigator per year, which amounts to annual investment in biomedical research of about $825 million. The institute has an endowment of $22.6 billion, making it the second-wealthiest philanthropic organization in the United States and the second-best endowed medical research foundation in the world. HHMI is the former owner of the Hughes Aircraft Company – an American aerospace firm which was divested to various firms over time. History The institute was ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
National Center For Biotechnology Information
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper. The NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for biomedical literature. Other databases include the NCBI Epigenomics database. All these databases are available online through the Entrez search engine. NCBI was directed by David Lipman, one of the original authors of the BLAST sequence alignment program and a widely respected figure in bioinformatics. GenBank NCBI had responsibility for making available the GenBan ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transfer-messenger RNA
Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with Small Protein B ( SmpB), Elongation Factor Tu ( EF-Tu), and ribosomal protein S1. In ''trans''-translation, tmRNA and its associated proteins bind to bacterial ribosomes which have stalled in the middle of protein biosynthesis, for example when reaching the end of a messenger RNA which has lost its stop codon. The tmRNA is remarkably versatile: it recycles the stalled ribosome, adds a proteolysis-inducing tag to the unfinished polypeptide, and facilitates the degradation of the aberrant messenger RNA. In the majority of bacteria these functions are carried out by standard one-piece tmRNAs. In other bacterial species, a permuted ''ssrA'' gene produces a two-piece tmRNA in which two separate RNA chains are joined by base-pairing. Dis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transfer RNA
Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino acid sequence of proteins. tRNAs genes from Bacteria are typically shorter (mean = 77.6 bp) than tRNAs from Archaea (mean = 83.1 bp) and eukaryotes (mean = 84.7 bp). The mature tRNA follows an opposite pattern with tRNAs from Bacteria being usually longer (median = 77.6 nt) than tRNAs from Archaea (median = 76.8 nt), with eukaryotes exhibiting the shortest mature tRNAs (median = 74.5 nt). Transfer RNA (tRNA) does this by carrying an amino acid to the protein synthesizing machinery of a cell called the ribosome. Complementation of a 3-nucleotide codon in a messenger RNA (mRNA) by a 3-nucleotide anticodon of the tRNA results in protein synthesis based on the mRNA code. As such, tRNAs are a necessary component of translation, the biological ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FASTA Format
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a near universal standard in the field of bioinformatics. The simplicity of FASTA format makes it easy to manipulate and parse sequences using text-processing tools and scripting languages like the R programming language, Python, Ruby, Haskell, and Perl. Original format & overview The original FASTA/ Pearson format is described in the documentation for the FASTA suite of programs. It can be downloaded with any free distribution of FASTA (see fasta20.doc, fastaVN.doc or fastaVN.me—where VN is the Version Number). In the original format, a sequence was represented as a series of lines, each o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GeneMark
GeneMark is a generic name for a family of ab initio gene prediction programs developed at the Georgia Institute of Technology in Atlanta. Developed in 1993, original GeneMark was used in 1995 as a primary gene prediction tool for annotation of the first completely sequenced bacterial genome of '' Haemophilus influenzae'', and in 1996 for the first archaeal genome of ''Methanococcus jannaschii''. The algorithm introduced inhomogeneous three-periodic Markov chain models of protein-coding DNA sequence that became standard in gene prediction as well as Bayesian approach to gene prediction in two DNA strands simultaneously. Species specific parameters of the models were estimated from training sets of sequences of known type (protein-coding and non-coding). The major step of the algorithm computes for a given DNA fragment posterior probabilities of either being "protein-coding" (carrying genetic code) in each of six possible reading frames (including three frames in complementary ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GLIMMER
In bioinformatics, GLIMMER (Gene Locator and Interpolated Markov ModelER) is used to find genes in prokaryotic DNA. "It is effective at finding genes in bacteria, archea, viruses, typically finding 98-99% of all relatively long protein coding genes". GLIMMER was the first system that used the interpolated Markov model to identify coding regions. The GLIMMER software is open source and is maintained by Steven Salzberg, Art Delcher, and their colleagues at the ''Center for Computational Biology'' at Johns Hopkins University. The original GLIMMER algorithms and software were designed by Art Delcher, Simon Kasif and Steven Salzberg and applied to bacterial genome annotation in collaboration with Owen White. Versions GLIMMER 1.0 First Version of GLIMMER "i.e., GLIMMER 1.0" was released in 1998 and it was published in the paper ''Microbial gene identification using interpolated Markov model''. Markov models were used to identify microbial genes in GLIMMER 1.0. GLIMMER considers the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Washington, D
Washington commonly refers to: * Washington (state), United States * Washington, D.C., the capital of the United States ** A metonym for the federal government of the United States ** Washington metropolitan area, the metropolitan area centered on Washington, D.C. * George Washington (1732–1799), the first president of the United States Washington may also refer to: Places England * Washington, Tyne and Wear, a town in the City of Sunderland metropolitan borough ** Washington Old Hall, ancestral home of the family of George Washington * Washington, West Sussex, a village and civil parish Greenland * Cape Washington, Greenland * Washington Land Philippines * New Washington, Aklan, a municipality *Washington, a barangay in Catarman, Northern Samar *Washington, a barangay in Escalante, Negros Occidental *Washington, a barangay in San Jacinto, Masbate *Washington, a barangay in Surigao City United States * Washington, Wisconsin (other) * Fort Washington (disambigu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GenBank
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 (NCBI; a part of the National Institutes of Health in the United States) as part of the International Nucleotide Sequence Database Collaboration (INSDC). GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 500,000 formally described species. The database started in 1982 by Walter Goad and Los Alamos National Laboratory. GenBank has become an important database for research in biological fields and has grown in recent years at an exponential rate by doubling roughly every 18 months. Release 250.0, published in June 2022, contained over 17 trillion nucleotide bases in more than 2,45 billion sequences. GenBank is built by direct submissions from individual laboratories, as well as from bulk submiss ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid resid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
