"Several specialized biological databases provide tools to identify andyze orthologous gene sequences. These resources employ approaches that can be generally cl.ified into those that are based on all pairwise sequence comparisons heuristic and those that use phylogenetic methods..However, gene order also degrades over evolutionary time. How well synteny will be able to effectively identify ancient orthologs remains to be seen. Gene Duplication Mechanisms and Orthologs. Gene duplications are a major force in genome evolution ..I am trying to find paralogous genes in a model organism Arabidopsis . To do that am using blast with the sequence for its own database. The first hit I get is the protein sequence aligned with it self using peptide - amino acid sequence which is .I have lots of contig hits from a transcriptome and need to figure out which one is orthologous to my query gene. Usually this is a very manual .
Related posts to identify orthologs
Other databases that provide eukaryotic orthologs include OrthoMCL, OrthoMaM for mammals, OrthologID and GreenPhylDB for plants. Tree-based phylogenetic approaches aim to distinguish speciation from gene duplication events by comparing gene trees with species trees, as implemented in resources such as TreeFam and LOFT..
To do that am using blast they by definition cannot be orthologs. the moment you go down that path and introduce multiple different parameters to identify .
187 and possible common ancestry, but they cannot unambiguously identify functional orthologs. 188 One way to track the functionality of thelogous genes after species split is to dissect 189 their expression patterns under a range of spatio-temporal and/or environmental conditions..
.uming conservation of specificity among orthologs and different specificity of paralogs, we identify residues which correlate with this grouping by specificity. The method is taking advantage of complete genomes to find multiple orthologs and paralogs..