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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 ...
PatternHunter is a commercially available homology search instrument software that uses sequence alignment techniques. It was initially developed in the year 2002 by three scientists: Bin Ma, John Tramp and Ming Li.
It detects homology by comparing a profile-HMM (a Hidden Markov model constructed explicitly for a particular search) to either a single sequence or a database of sequences. Sequences that score significantly better to the profile-HMM compared to a null model are considered to be homologous to the sequences that were used to construct the ...
As with anatomical structures, sequence homology between protein or DNA sequences is defined in terms of shared ancestry. Two segments of DNA can have shared ancestry because of either a speciation event or a duplication event . Homology among proteins or DNA is typically inferred from their sequence similarity.
The critical first step in homology modeling is the identification of the best template structure, if indeed any are available. The simplest method of template identification relies on serial pairwise sequence alignments aided by database search techniques such as FASTA and BLAST.
[3] [30] This concept has been used, for example, to search all E. coli protein sequences for homology in other genomes and find over 6000 pairs of sequences with shared homology to single proteins in another genome, indicating potential interaction between each of the pairs. [30]
Orthology or paralogy inference requires an assessment of sequence homology, usually via sequence alignment. Phylogenetic analyses and sequence alignment are often considered jointly, as phylogenetic analyses using DNA or RNA require sequence alignment and alignments themselves often represent some hypothesis of homology.
Homology-based gene prediction based on amino acid and intron position conservation as well as RNA-Seq data [14] [15] GENIUS II Links ORFs in complete genomes to protein 3D structures: Prokaryotes, Eukaryotes [16] geneid: Program to predict genes, exons, splice sites, and other signals along DNA sequences: Eukaryotes [17] GeneParser