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HomoloGene
HomoloGene, a tool of the United States National Center for Biotechnology Information (NCBI), is a system for automated detection of homologs (similarity attributable to descent from a common ancestor) among the annotated genes of several completely sequenced eukaryotic genomes. The HomoloGene processing consists of the protein analysis from the input organisms. Sequences are compared using blastp, then matched up and put into groups, using a taxonomic tree built from sequence similarity, where closer related organisms are matched up first, and then further organisms are added to the tree. The protein alignments are mapped back to their corresponding DNA sequences, and then distance metrics as molecular distances Jukes and Cantor (1969), Ka/Ks ratio can be calculated. The sequences are matched up by using a heuristic algorithm for maximizing the score globally, rather than locally, in a bipartite matching (see complete bipartite graph). And then it calculates the statistical sig ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ortholog
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal (or lateral) gene transfer event (xenologs). Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. Significant similarity is strong evidence that two sequences are related by evolutionary changes from a common ancestral sequence. Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. Identity, similarity, and conservation The term "percent homology" is often used to mean "sequence similarity”, that is the percentage of identical residues (''percent identity''), or the percentage of residues conserved with similar physicochemical properties ... [...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 GenBank DNA seq ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Xenopus Tropicalis
The western clawed frog (''Xenopus tropicalis'') is a species of frog in the family Pipidae, also known as tropical clawed frog. It is the only species in the genus ''Xenopus'' to have a diploid genome. Its genome has been sequenced, making it a significant model organism for genetics that complements the related species ''Xenopus laevis'' (the African clawed frog), a widely used vertebrate model for developmental biology. ''X. tropicalis'' also has a number of advantages over ''X. laevis'' in research, such as a much shorter generation time (<5 months), smaller size ( body length), and a larger number of eggs per . It is found in , |
Plants
Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae exclude the fungi and some algae, as well as the prokaryotes (the archaea and bacteria). By one definition, plants form the clade Viridiplantae (Latin name for "green plants") which is sister of the Glaucophyta, and consists of the green algae and Embryophyta (land plants). The latter includes the flowering plants, conifers and other gymnosperms, ferns and their allies, hornworts, liverworts, and mosses. Most plants are multicellular organisms. Green plants obtain most of their energy from sunlight via photosynthesis by primary chloroplasts that are derived from endosymbiosis with cyanobacteria. Their chloroplasts contain chlorophylls a and b, which gives them their green color. Some plants are parasitic or mycotrophic and have lost the ab ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Neurospora Crassa
''Neurospora crassa'' is a type of red bread mold of the phylum Ascomycota. The genus name, meaning "nerve spore" in Greek, refers to the characteristic striations on the spores. The first published account of this fungus was from an infestation of French bakeries in 1843. ''Neurospora crassa'' is used as a model organism because it is easy to grow and has a haploid life cycle that makes genetic analysis simple since recessive traits will show up in the offspring. Analysis of genetic recombination is facilitated by the ordered arrangement of the products of meiosis in ''Neurospora'' ascospores. Its entire genome of seven chromosomes has been sequenced. ''Neurospora'' was used by Edward Tatum and George Wells Beadle in their experiments for which they won the Nobel Prize in Physiology or Medicine in 1958. Beadle and Tatum exposed ''N. crassa'' to x-rays, causing mutations. They then observed failures in metabolic pathways caused by errors in specific enzymes. This led them to p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Magnaporthe Grisea
''Magnaporthe grisea'', also known as rice blast fungus, rice rotten neck, rice seedling blight, blast of rice, oval leaf spot of graminea, pitting disease, ryegrass blast, Johnson spot, neck blast, wheat blast, and Imochi ( Japanese:稲熱) is a plant-pathogenic fungus and model organism that causes a serious disease affecting rice. It is now known that ''M. grisea'' consists of a cryptic species complex containing at least two biological species that have clear genetic differences and do not interbreed. Complex members isolated from '' Digitaria'' have been more narrowly defined as ''M. grisea''. The remaining members of the complex isolated from rice and a variety of other hosts have been renamed ''Magnaporthe oryzae'', within the same ''M. grisea'' complex. Confusion on which of these two names to use for the rice blast pathogen remains, as both are now used by different authors. Members of the ''Magnaporthe grisea'' complex can also infect other agriculturally important cere ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Eremothecium Gossypii
(also known as Ashbya gossypii) is a filamentous fungus or mold closely related to yeast, but growing exclusively in a filamentous way. It was originally isolated from cotton as a pathogen causing stigmatomycosis by Ashby and Nowell in 1926. This disease affects the development of hair cells in cotton bolls and can be transmitted to citrus fruits, which thereupon dry out and collapse (dry rot disease). In the first part of the 20th century, and two other fungi causing stigmatomycosis (, ) made it virtually impossible to grow cotton in certain regions of the subtropics, causing severe economical losses. Control of the spore-transmitting insects cotton stainer() and - permitted full eradication of infections. was recognized as a natural overproducer of riboflavin (vitamin B2), which protects its spores against ultraviolet light. This made it an interesting organism for industries, where genetically modified strains are still used to produce this vitamin. as a model organism ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Kluyveromyces Lactis
''Kluyveromyces lactis'' is a '' Kluyveromyces'' yeast commonly used for genetic studies and industrial applications. Its name comes from the ability to assimilate lactose and convert it into lactic acid. ''Kluyveromyces lactis'' (formerly ''Saccharomyces lactis'') is a yeast which has the ability to assimilate lactose and convert it into lactic acid. ''K. lactis'' and other organisms i.e., ''Aspergillus niger'' var awamori and ''Escherichia coli'' K-12 are grown in fermenters to produce chymosin ( rennet) on a commercial scale; this rennet, which replaces the conventional form obtained from slaughtered animals, is now widely used in cheese production. Yeasts and fungi are ideal organisms for comparative genomic studies in eukaryotes because of their small and compact genomes and because they include a number of species such as ''Neurospora crassa'', ''Saccharomyces cerevisiae'' and ''Schizosaccharomyces pombe'', that have been, and continue to be, used extensively in genetic s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Schizosaccharomyces Pombe
''Schizosaccharomyces pombe'', also called "fission yeast", is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically measure 3 to 4 micrometres in diameter and 7 to 14 micrometres in length. Its genome, which is approximately 14.1 million base pairs, is estimated to contain 4,970 protein-coding genes and at least 450 non-coding RNAs. These cells maintain their shape by growing exclusively through the cell tips and divide by medial fission to produce two daughter cells of equal size, which makes them a powerful tool in cell cycle research. Fission yeast was isolated in 1893 by Paul Lindner from East African millet beer. The species name ''pombe'' is the Swahili word for beer. It was first developed as an experimental model in the 1950s: by Urs Leupold for studying genetics, and by Murdoch Mitchison for studying the cell cycle. Paul Nurse, a fission yeast ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Saccharomyces Cerevisiae
''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been originally isolated from the skin of grapes. It is one of the most intensively studied eukaryotic model organisms in molecular and cell biology, much like '' Escherichia coli'' as the model bacterium. It is the microorganism behind the most common type of fermentation. ''S. cerevisiae'' cells are round to ovoid, 5–10 μm in diameter. It reproduces by budding. Many proteins important in human biology were first discovered by studying their homologs in yeast; these proteins include cell cycle proteins, signaling proteins, and protein-processing enzymes. ''S. cerevisiae'' is currently the only yeast cell known to have Berkeley bodies present, which are involved in particular secretory pathways. Antibodies against ''S. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fungi
A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from the other eukaryotic kingdoms, which by one traditional classification include Plantae, Animalia, Protozoa, and Chromista. A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists is chitin in their cell walls. Fungi, like animals, are heterotrophs; they acquire their food by absorbing dissolved molecules, typically by secreting digestive enzymes into their environment. Fungi do not photosynthesize. Growth is their means of mobility, except for spores (a few of which are flagellated), which may travel through the air or water. Fungi are the principal decomposers in ecological systems. These and other differences place fungi in a single group of related organisms, named the ''Eumycota'' (''t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Caenorhabditis Elegans
''Caenorhabditis elegans'' () is a free-living transparent nematode about 1 mm in length that lives in temperate soil environments. It is the type species of its genus. The name is a blend of the Greek ''caeno-'' (recent), ''rhabditis'' (rod-like) and Latin ''elegans'' (elegant). In 1900, Maupas initially named it '' Rhabditides elegans.'' Osche placed it in the subgenus ''Caenorhabditis'' in 1952, and in 1955, Dougherty raised ''Caenorhabditis'' to the status of genus. ''C. elegans'' is an unsegmented pseudocoelomate and lacks respiratory or circulatory systems. Most of these nematodes are hermaphrodites and a few are males. Males have specialised tails for mating that include spicules. In 1963, Sydney Brenner proposed research into ''C. elegans,'' primarily in the area of neuronal development. In 1974, he began research into the molecular and developmental biology of ''C. elegans'', which has since been extensively used as a model organism. It was the first mult ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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