Accurate predictions of orthology and paralogy relationships are necessary to infer human molecular function from experiments in model organisms. Previous genome-scale approaches to predicting these relationships have been limited by their use of protein similarity and their failure to take

protein translation. Numerous miRNAs have been discovered via deep sequencing. Many miRNAs are produced from multiple genome sites. These miRNAs are grouped into paralogous families of miRNAs that generate the same major mature form within organisms. Currently, no method of distinguishing the expression

We developed a user-friendly program, Genome Profiler (GeP), to refine whole-genome multilocus sequence typing analysis by addressing gene paralogy with conserved gene neighborhoods. In comparison to similar programs, GeP produced overall the best results in terms of accuracy and is thus a useful

and lenore.cowen@tufts.edu Current automated computational methods to assign functional labels to unstudied genes often involve transferring annotation from orthologous or paralogous genes, however such genes can evolve divergent functions, making such transfer inappropriate. We consider

(eEF-1a), archaebacterial EF-1a (aEF-1a) and two eukaryote-speci®c EF-1a paralogsÐeukaryotic release factor 3 (eRF3) and Hsp70 subfamily B sup-pressor 1 (HBS1). Overall, the evolutionary modes of aEF-1a, HBS1 and eRF3 appear to signi®cantly differ from that of eEF-1a. However, functionally divergent

yThese authors contributed equally to this work. zThese authors made shared contributions as senior author.

The primary signal of sex determination in the honeybee, the complementary sex determiner (csd) gene, evolved from a gene duplication event from an ancestral copy of the fem gene. Recently, other paralogs of the fem gene have been identified in several ant and bumblebee genomes. This discovery

-random arrangements can arise by two distinct evolutionary processes: duplications of DNA sequences that give rise to clusters of genes sharing both sequence similarity and common sequence features and the migration together of genes related by function, but not by common descent [1,2,3]. To provide a background

, as analyzed here for the highly homologous paralogs Foxa1 and Foxa2 transcriptional regulators. We determine by genome-wide location analysis (ChIP-Seq) that, although Foxa1 and Foxa2 share a large fraction of binding sites in the liver, each protein also occupies distinct regulatory elements in vivo. Foxa1

relationships between duplicates, those arising from SSD are usually unbalanced and are expected to follow different evolutionary dynamics than those formed by WGD. To dissect the role of the mechanism of duplication in these differential dynamics and determine whether this role was shared across species, we