A central goal in molecular evolution is to understand the ways in which genes and proteins
evolve in response to changing environments. In the absence of intact DNA from fossils …

Abstract The University of California Santa Cruz (UCSC) Genome Browser (http://genome.
ucsc. edu) offers online public access to a growing database of genomic sequence and …

Background Molecular methods of species delineation are rapidly developing and widely
considered as fast and efficient means to discover species and face the'taxonomic …

Recombination allows different parts of the genome to have different genealogical histories.
When a species splits in two, allelic lineages sort into the two descendant species, and this …

Cis-regulatory modules contain multiple transcription factor (TF)-binding sites and integrate
the effects of each TF to control gene expression in specific cellular contexts. Transposable …

MicroRNAs (miRNA) are short single-stranded RNA molecules derived from hairpin-forming
precursors that play a crucial role as post-transcriptional regulators in eukaryotes and …

Abstract Background The Monte Carlo simulation of sequence evolution is routinely used to
assess the performance of phylogenetic inference methods and sequence alignment …

The computational inference of ancestral genomes consists of five difficult steps: identifying
syntenic regions, inferring ancestral arrangement of syntenic regions, aligning multiple …

Protein evolution relies on designing a library of sequences that capture meaningful
functional diversity in a limited number of protein variants. Several approaches take …

Sequences derived from the Long INterspersed Element-1 (L1) family of retrotransposons
occupy at least 17% of the human genome, with 67 distinct subfamilies representing …