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	Definition of Homolog, Ortholog and Paralog (Site not responding. Last check: 2007-11-05)
		Orthologs are genes in different species that evolved from a common ancestral gene by speciation.
		Identification of orthologs is critical for reliable prediction of gene function in newly sequenced genomes.
		Orthologs retain the same function in the course of evolution, whereas paralogs evolve new functions, even if these are related to the original one.
	homepage.usask.ca /~ctl271/857/def_homolog.shtml (191 words)

	BioMed Central \| Full text \| Improving the specificity of high-throughput ortholog prediction
		Ortholog prediction is an important facet of comparative genomics and is frequently used in genome annotation, gene function characterization, evolutionary genomics, and in the identification of conserved regulatory elements.
		Orthologs are commonly defined as genes that have diverged after a speciation event [1], whereas genes that have diverged after a gene duplication event, either before a speciation event (out-paralogs) or after a speciation event (in-paralogs), are collectively known as paralogs.
		Orthologs between these three species (and other sets of species subsequently examined) were predicted using a transitive RBH approach, applied to the deduced proteins from complete genome sequences [10-12].
	www.biomedcentral.com /1471-2105/7/270 (9581 words)

	Ortholog - Wikipedia, the free encyclopedia
		Classically, orthologs are genes in different species which evolved from a common ancestral gene.
		Due to their separation following a speciation event, orthologs may diverge, but usually have similarity at the seqence and structure levels; furthermore, orthologs usually have similar functions.
		The term "ortholog" was coined in 1970 to describe two genes in two different species that originated from a common ancestor.
	en.wikipedia.org /wiki/Orthologue (305 words)

	Inparanoid: Eukaryotic Ortholog Groups
		By definition orthologs between 2 species have evolved from one single gene in their ancient common ancestor.
		Ortholog clusters in the InParanoid are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied.
		The Inparanoid eukaryotic ortholog database is a collection of pairwise comparisons between 17 whole genomes; Anopheles gambiae, Caenorhabditis briggsae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Takifugu rubripes, Gallus gallus, Homo sapiens, Mus musculus, Pan troglodytes, Rattus norvegicus, Oryza sativa, Plasmodium falciparum, Arabidopsis thaliana, Escherichia coli, Saccharomyces cerevisiae and Schizosaccharomyces pombe.
	inparanoid.cgb.ki.se /ehelp.html (845 words)

	Ortholog
		An equivalent gene in different organisms, based on similarity of genetic sequence and the degree of correlation of conserved sequences.
		Functional genes in animals such as mice have been used to help find the similarly functional genes in humans — the human orthologs of the animal gene.
		The idea of conserved sequences generally relies on the assumption that organisms share a common genetic ancestry, but is equally well explained by the inference of common design.
	www.iscid.org /encyclopedia/Ortholog (89 words)

	Ortholog - Wikipedia, the free encyclopedia
		Orthologous sequences provide useful information in taxonomic classification studies of organisms.
		The pattern of genetic divergence can be used to trace the relatedness of organisms.
		Conversely, an organism that is further removed evolutionarily from another organism can display a greater variation in the sequence of the two orthologs being studied.
	en.wikipedia.org /wiki/Ortholog (305 words)

	The Zebrafish Database Class: ORTHOLOG (Site not responding. Last check: 2007-11-05)
		Role: The ORTHOLOG class was established to represent, in a limited fashion, orthologies between zebrafish and other organisms.
		Each ORTHOLOG record represents one such relationship, associating a particular cloned gene in zebrafish with its ortholog in another organism.
		Rather than listing just the name of the ortholog in the other organism, we also want to “cache” some additional information about it like, for example, its map location and its accession number to the database for the other species.
	zfin.org /zf_info/dbase/PAPERS/ZFIN_DataModel/sectionii_6.html (293 words)

	[No title]
		3292814954 NIL NIL) DBLINKS - (ECOO157CYC Z4018 Ortholog
		3292814954 NIL NIL) DBLINKS - (ECOO157CYC SPY Ortholog
		3292814954 NIL NIL) DBLINKS - (ECOO157CYC Z2250 Ortholog
	www.binf.ku.dk /~rasmus/genes.dat (17100 words)

	Genome Biology \| Abstract \| Benchmarking ortholog identification methods using functional genomics data
		Various methods are used to analyze cross-species orthologous relationships according to an operational definition of orthology.
		To identify protein pairs with the highest possible functional similarity, it is important to qualify ortholog identification methods.
		In general, we observed a sensitivity/selectivity trade-off: the functional similarity scores per orthologous pair of sequences become higher when the number of proteins included in the ortholog groups decreases.
	genomebiology.com /2006/7/4/R31/abstract (289 words)

	Evolution of vertebrate E protein transcription factors: comparative analysis of the E protein gene family in Takifugu ...
		Within the E2A branch, the genes with single spliced transcript and two alternatively spliced transcripts (E12/E47 orthologs) are indicated as groups 1 and 2, respectively.
		E2A genes in Takifugu: an ortholog and a paralog.
		the identification of the Takifugu 233 gene as an HEB ortholog
	physiolgenomics.physiology.org /cgi/content/full/21/2/144 (3103 words)

	ARS \| Publication request: CLONING AND CHARACTERIZATION OF A FLORICAULA/LEAFY ORTHOLOG, PFL, IN POLYGAMOUS PAPAYA (Site not responding. Last check: 2007-11-05)
		The network of flower meristem identity genes that control the transition of plants from vegetative to reproductive states is apparently conserved among plants having flowers with both male and female sex organs (hermaphrodite), but has been inadequately studied in plants such as papaya that have different sex forms (male, female, or hermaphrodite).
		We used the Arabidopsis LFY flowering gene cDNA clone to isolate an orthologous gene, PFL, from papaya and showed that it is expressed at a relatively low level in vegetative tissues and at a higher level in flower buds of all three sex types.
		We used Arabidopsis LFY cDNA as a probe to clone and sequence a papaya ortholog of LFY, PFL.
	www.ars.usda.gov /research/publications/publications.htm?seq_no_115=180652 (478 words)

	HSLS: OrthoMCL-DB -- querying a comprehensive multi-species collection of ortholog groups (Site not responding. Last check: 2007-11-05)
		The OrthoMCL database houses ortholog group predictions for 55 species, including 16 bacterial and 4 archaeal genomes representing phylogenetically diverse lineages, and most currently available complete eukaryotic genomes: 24 unikonts (12 animals, 9 fungi, microsporidium, Dictyostelium, Entamoeba), 4 plants oralgae and 7 apicomplexan parasites.
		The ortholog database may be queried based on protein or group accession numbers, keyword descriptions or BLAST similarity.
		Information for ortholog groups includes the phyletic profile, the list of member proteins and a multiple sequence alignment, a statistical summary and graphical view of similarities, and a graphical representation of domain architecture.
	www.hsls.pitt.edu /guides/genetics/tools/genomics/genetic_information_retrieval/URL1139607191/info (285 words)

	OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes -- Li et al. 13 (9): 2178 -- Genome Research
		proteins is orthologous to a protein in another species.
		The net result of this normalization is to correct for systematic differences in comparisons between two species (e.g., differences attributable to nucleotide composition bias), and when i = j, to minimize the impact of "recent" paralogs (duplication within a given species) on the clustering of cross-species orthologs.
		Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA).
	www.genome.org /cgi/content/full/13/9/2178 (6368 words)

	OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups -- Chen et al. 34 (Supplement 1): ...
		ortholog database may be queried based on protein or group accession
		Ortholog groups are displayed to reflect patterns of phyletic
		Rows in the phyletic pattern profile table represent bacteria, archaea, single-cellular eukaryotes and multi-cellular eukaryotes (plants and animals); each box represents a single species, with fl or white background denoting presence or absence in the ortholog group, and the number of protein sequences found in the ortholog group listed.
	nar.oxfordjournals.org /cgi/content/full/34/suppl_1/D363 (2759 words)

	Supplementary Information for Coghlan and Wolfe (2004)
		Note that introns are numbered from left to right along the sense strand of the gene (not from 5' to 3' in the gene).
		(ortholog C09H10.3, complex I : NADH to ubiquinone)
		(ortholog T08A11.2, homolog of human splicing factor 3B subunit 1)
	wolfe.gen.tcd.ie /avril/introns.html (366 words)

	ARS \| Publication request: CLONING AND CHARACTERIZATION OF A PAPAYA SUPERMAN ORTHOLOG (Site not responding. Last check: 2007-11-05)
		Technical Abstract: The floral regulatory gene SUPERMAN (SUP) is reported to be an upstream negative regulator of the B function organ-identity genes, acting in the forth whorl to establish a boundary between stamen and carpel whorls.
		Sequence analysis revealed that the 3.5K positive fragment BAC clone encodes a protein similar to that encoded by the entire coding region of the Arabidopsis thaliana SUP gene.
		At the protein level, the papaya SUP ortholog, PSUP, shares 43% identity and 52% similarity with Arabidopsis thaliana SUP gene.
	www.ars.usda.gov /research/publications/publications.htm?SEQ_NO_115=166578 (314 words)

	Conserved Ortholog Set (COS) markers
		We have used a computational method to screen the tomato EST database against the arabidopsis genome sequence in order to find a set of highly conserved, single copy genes which can be used as markers for comparative mapping between the tomato and arabidopsis genomes.
		In this section of SGN, you will find sequence and clone information for each of these COS markers as well as their matching counterpart in the arabidopsis genome.
		ESTs that pass all these criteria are classified as conserved orthologs, all others are considered potentially paralogous and eliminated.
	www.sgn.cornell.edu /markers/cos_markers.pl (481 words)

	Glossary
		COGs Clusters of Orthologous Groups (of proteins) were delineated by comparing protein sequences from completely sequenced genomes.
		Each COG consists of individual proteins or groups of paralogs from at least three lineages and thus corresponds to an ancient conserved domain.
		ortholog Orthology describes genes in different species that derive from a single ancestral gene in the last common ancestor of the respective species.
	www.ncbi.nlm.nih.gov /books/bv.fcgi?call=bv.View..ShowSection&rid=handbook.glossary.1237 (9427 words)

	BioBIKE: Ortholog-of (Site not responding. Last check: 2007-11-05)
		"Ortholog" is defined as Two-way-ortholog-of, where protein A in organism X is the best blast hit of protein B in organism Y and vice versa, both hits better than a cutoff E-value
		Only one ortholog is returned for a gene or protein.
		If entity is a contig or replicon, then a list is returned consisting of orthologs in the given organism of all proteins in the given contig or replicon
	ramsites.net /~biobike/documentation/source/Ortholog-of.html (224 words)

	CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of ...
		CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes -- Jegga et al.
		of regulatory regions of individual orthologous gene pairs (7–12).
		Genomic regions of orthologous genes are retrieved from UCSC
	nar.oxfordjournals.org /cgi/content/full/33/suppl_2/W408 (2532 words)

	[No title]
		B0024.8 B0024.8 Putative ortholog of C. elegans B0024.5 gene product B0024.9 B0024.9 Member of the thioredoxin protein family, which are small enzymes involved in redox reactions, has low similarity to thioredoxin I (S. cerevisiae Trx1p) thioredoxin; This gene encodes a protein predicted by Eisenberg and coworkers, with 52% accuracy, to be mitochondrial.
		B0025.2 B0025.2 Protein with high similarity to thyroid receptor interacting protein 15 (human TRIP15), which is a nuclear hormone transcription corepressor, contains a PCI (proteasome, COP9-complex and eIF3) or PINT (Proteasome, Int-6, Nip-1 and TRIP-15) domain csn-2 encodes a homolog of COP9 signalosome complex subunit 2 that affects embryonic viability and growth rate.
		C02G6.1 C02G6.1 Member of the insulinase (peptidase M16) family, has moderate similarity to insulin-degrading enzyme (insulysin, rat Ide), which is a metallopeptidase that degrades insulin, amyloid beta (rat App), insulin-like growth factors, and natriuretic peptides peptidase; This gene encodes a protein predicted by Eisenberg and coworkers, with 68% accuracy, to be mitochondrial.
	elegans.uky.edu /MA/progs/gene_descriptions.10-05.txt (733 words)

	CiteULike: Tag ortholog (Site not responding. Last check: 2007-11-05)
		Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs
		Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins.
		Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.
	www.citeulike.org /tag/ortholog (178 words)

	VFL, the Grapevine FLORICAULA/LEAFY Ortholog, Is Expressed in Meristematic Regions Independently of Their Fate -- ...
		VFL, the Grapevine FLORICAULA/LEAFY Ortholog, Is Expressed in Meristematic Regions Independently of Their Fate -- Carmona et al.
		orthologs have been cloned and characterized in several woody
		orthologs have been reported to be expressed in developing leaves
	www.plantphysiol.org /cgi/content/full/130/1/68 (5045 words)

	[Genome] Human and Mouse specific and ortholog genes (Site not responding. Last check: 2007-11-05)
		Previous message: [Genome] Human and Mouse specific and ortholog genes
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		Together with mmBlastTab, they may help you to get get the lists of genes you want.
	www.cse.ucsc.edu /pipermail/genome/2005-January/006486.html (233 words)

	COS (Conserved Ortholog Set) Candidates
		To study synteny between different life organisms very important to select the set of conserved ortholog markers (genes).
		Because of multiple gene duplications it is hard to distinguish orthologs from paralogs.
		Final set with clusters where Arabidopsis gene is represented as a single node can be considered as a true Conserved Orthologs Set (COS).
	cgpdb.ucdavis.edu /COS_Markers/COS_Markers.html (482 words)

	Identification, Analysis, and Utilization of Conserved Ortholog Set Markers for Comparative Genomics in Higher Plants ...
		Identification, Analysis, and Utilization of Conserved Ortholog Set Markers for Comparative Genomics in Higher Plants -- Fulton et al.
		However, one cannot assume that it is an ortholog, because
		Thus, orthologs may not be distinguished easily from paralogs.
	www.plantcell.org /cgi/content/full/14/7/1457 (5264 words)

	SGD Glossary Terms
		Location of genes on the same chromosome, e.g., genes with a common chromosomal location are said to be part of the same syntenic group.
		Also used to refer to conservation of gene order across species, e.g., if orthologous genes are located together and in the same relative order in different species, then the block of genes is said to be syntenic between the species.
		A genetic interaction in which a combination of mutations in two or more genes of a single strain results in a phenotype that is different in degree or nature from the phenotypes conferred by the individual mutations.
	genome-www.stanford.edu /Saccharomyces/help/glossary.html (10452 words)

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