What is Orthology analysis?
Within homology, the orthology analyses, that consist in finding out if a pair of homologous genes are orthologs—i.e., resulting from a speciation—or paralogs—i.e., resulting from a gene duplication—is very important in computational biology, genome annotation, and phylogenetic inference (Ullah et al., 2015).
What is Orthology in bioinformatics?
Orthologs. Orthologs are specific gene sequences that are closely related between two entirely different species, but often have the same functions. Separated by a speciation event where a species diverges into two separate species, divergent copies of a solitary gene result in the orthologous homologous sequence.
What are cluster of orthologous groups?
Database Description The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on phylogenetic classification of the proteins encoded in complete genomes. Each COGs includes proteins that are inferred to be orthologs (direct evolutionary counterparts).
What is Orthologist?
Orthology is the study of the right use of words in language. The word comes from Greek ortho- (“correct”) and -logy (“science of”). This science is a place where psychology, philosophy, linguistics, and many other fields of learning come together. And hence the person specialise in this field is called orthologist.
What is a orthologous gene?
Orthologs are genes in different species that evolved from a common ancestral gene by speciation, and, in general, orthologs retain the same function during the course of evolution. Identification of orthologs is a critical process for reliable prediction of gene function in newly sequenced genomes.
Are alleles paralogs?
Orthologous and paralogous genes are two types of homologous genes, that is, genes that arise from a common DNA ancestral sequence. Orthologous genes diverged after a speciation event, while paralogous genes diverge from one another within a species.
What is COG classification?
The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on a phylogenetic classification of the proteins encoded in 21 complete genomes of bacteria, archaea and eukaryotes (http://www.ncbi.nlm.nih.gov/COG ).
How many clusters of orthologous groups are there?
The COG database collection consists of 138,458 proteins from 66 genomes. These proteins form 4873 COGs. As noted above, these COGs, though listed in the new version, has no website function. The KOG sets contain 4,852 clusters of orthologs, utilizing 59,838 proteins.
How are orthologous groups assigned to a project?
Orthologous Groups are assigned to the project using the EggNOG database (section 2.1). Since EggNOG does not provide an API to assign the annotation directly from their REST service, we use UniProt RESTful service API, which contains the information of the Orthologous Group via EggNOG.
How are orthologous groups used in Evolutionary Inference?
Similarity information has multiple uses, such as sequence annotation or evolutionary inference. A Cluster of Orthologous Group (COG) corresponds to a group of proteins that share a high level of sequence similarity. Sequence similarity, in the vast majority of the cases, can be associated to evolutionary convergence.
Which is better orthologous groups or UniProtKB?
The Orthologous Group Annotation will have a better performance if the Blast is executed against the UniProtKb database. In case the Blast is performed against the nr database, the result of the Orthologous Group Annotation will be satisfactory, but the quality will still be lower than if UniProtKb was used as the Blast database.
