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OrthoFinder
OrthoFinder is a Command-line_interface, command-line software tool for Bioinformatics#Comparative_genomics, comparative genomics. OrthoFinder determines the correspondence between genes in different organisms (also known as orthology analysis). This correspondence provides a framework for understanding the evolution of life on Earth, and enables the extrapolation and transfer of biological knowledge between organisms. OrthoFinder takes FASTA files of protein sequences as input (one per species) and as output provides: * Protein family, Orthogroups * Rooted Phylogenetic_tree, Phylogenetic trees of all orthogroups * A rooted species tree for the set of species included in the input dataset * Hierarchical orthogroups for each node in the species tree * Sequence_homology, Orthologs between all species * Gene duplication events mapped to branches in the species tree * Comparative genomic statistics As of August 2021, the tool has been referenced by more than 1500 published studie ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OrthoFinder Workflow
OrthoFinder is a Command-line_interface, command-line software tool for Bioinformatics#Comparative_genomics, comparative genomics. OrthoFinder determines the correspondence between genes in different organisms (also known as orthology analysis). This correspondence provides a framework for understanding the evolution of life on Earth, and enables the extrapolation and transfer of biological knowledge between organisms. OrthoFinder takes FASTA files of protein sequences as input (one per species) and as output provides: * Protein family, Orthogroups * Rooted Phylogenetic_tree, Phylogenetic trees of all orthogroups * A rooted species tree for the set of species included in the input dataset * Hierarchical orthogroups for each node in the species tree * Sequence_homology, Orthologs between all species * Gene duplication events mapped to branches in the species tree * Comparative genomic statistics As of August 2021, the tool has been referenced by more than 1500 published studie ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Clustering
In bioinformatics, sequence clustering algorithms attempt to group biological sequences that are somehow related. The sequences can be either of genomic, "transcriptomic" ( ESTs) or protein origin. For proteins, homologous sequences are typically grouped into families. For EST data, clustering is important to group sequences originating from the same gene before the ESTs are assembled to reconstruct the original mRNA. Some clustering algorithms use single-linkage clustering, constructing a transitive closure of sequences with a similarity over a particular threshold. UCLUST and CD-HIT use a greedy algorithm that identifies a representative sequence for each cluster and assigns a new sequence to that cluster if it is sufficiently similar to the representative; if a sequence is not matched then it becomes the representative sequence for a new cluster. The similarity score is often based on sequence alignment. Sequence clustering is often used to make a non-redundant set of r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Family
A protein family is a group of evolutionarily related proteins. In many cases, a protein family has a corresponding gene family, in which each gene encodes a corresponding protein with a 1:1 relationship. The term "protein family" should not be confused with Family (biology), family as it is used in taxonomy. Proteins in a family descend from a common ancestor and typically have similar protein structure, three-dimensional structures, functions, and significant Sequence homology, sequence similarity. The most important of these is sequence similarity (usually amino-acid sequence), since it is the strictest indicator of homology and therefore the clearest indicator of common ancestry. A fairly well developed framework exists for evaluating the significance of similarity between a group of sequences using sequence alignment methods. Proteins that do not share a common ancestor are very unlikely to show statistically significant sequence similarity, making sequence alignment a powerf ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Homology
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] |
Sequence Homology
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] |
Linux
Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which includes the kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name "GNU/Linux" to emphasize the importance of GNU software, causing some controversy. Popular Linux distributions include Debian, Fedora Linux, and Ubuntu, the latter of which itself consists of many different distributions and modifications, including Lubuntu and Xubuntu. Commercial distributions include Red Hat Enterprise Linux and SUSE Linux Enterprise. Desktop Linux distributions include a windowing system such as X11 or Wayland, and a desktop environment such as GNOME or KDE Plasma. Distributions intended for ser ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GNU General Public License
The GNU General Public License (GNU GPL or simply GPL) is a series of widely used free software licenses that guarantee end users the Four Freedoms (Free software), four freedoms to run, study, share, and modify the software. The license was the first copyleft for general use and was originally written by the founder of the Free Software Foundation (FSF), Richard Stallman, for the GNU Project. The license grants the recipients of a computer program the rights of the Free Software Definition. These GPL series are all copyleft licenses, which means that any derivative work must be distributed under the same or equivalent license terms. It is more restrictive than the GNU Lesser General Public License, Lesser General Public License and even further distinct from the more widely used permissive software licenses BSD licenses, BSD, MIT License, MIT, and Apache License, Apache. Historically, the GPL license family has been one of the most popular software licenses in the free and open ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Command-line Interface
A command-line interpreter or command-line processor uses a command-line interface (CLI) to receive commands from a user in the form of lines of text. This provides a means of setting parameters for the environment, invoking executables and providing information to them as to what actions they are to perform. In some cases the invocation is conditional based on conditions established by the user or previous executables. Such access was first provided by computer terminals starting in the mid-1960s. This provided an interactive environment not available with punched cards or other input methods. Today, many users rely upon graphical user interfaces and menu-driven interactions. However, some programming and maintenance tasks may not have a graphical user interface and use a command line. Alternatives to the command-line interface include text-based user interface menus (for example, IBM AIX SMIT), keyboard shortcuts, and various desktop metaphors centered on the pointer (usual ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Software Tool
A programming tool or software development tool is a computer program that software developers use to create, debug, maintain, or otherwise support other programs and applications. The term usually refers to relatively simple programs, that can be combined to accomplish a task, much as one might use multiple hands to fix a physical object. The most basic tools are a source code editor and a compiler or interpreter, which are used ubiquitously and continuously. Other tools are used more or less depending on the language, development methodology, and individual engineer, often used for a discrete task, like a debugger or profiler. Tools may be discrete programs, executed separately – often from the command line – or may be parts of a single large program, called an integrated development environment (IDE). In many cases, particularly for simpler use, simple ad hoc techniques are used instead of a tool, such as print debugging instead of using a debugger, manual timing (of overal ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FASTA
FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics. History The original FASTA program was designed for protein sequence similarity searching. Because of the exponentially expanding genetic information and the limited speed and memory of computers in the 1980s heuristic methods were introduced aligning a query sequence to entire data-bases. FASTA, published in 1987, added the ability to do DNA:DNA searches, translated protein:DNA searches, and also provided a more sophisticated shuffling program for evaluating statistical significance. There are several programs in this package that allow the alignment of protein sequences and DNA sequences. Nowadays, increased computer performance makes it possible to perform searches for local alignment detection in a database using the Smith–Waterman algorithm. FASTA is pronounced "fas ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetic Tree
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. All life on Earth is part of a single phylogenetic tree, indicating common ancestry. In a ''rooted'' phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetics. ''Unrooted'' trees illustrate only the relatedness of the leaf nodes and do not require the ancestral root to b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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