title: eShadow: a tool for comparing closely related sequences.
abstract: Primate sequence comparisons are difficult to interpret due to the high degree of sequence similarity shared between such closely related species. Recently, a novel method, phylogenetic shadowing, has been pioneered for predicting functional elements in the human genome through the analysis of multiple primate sequence alignments. We have expanded this theoretical approach to create a computational tool, eShadow, for the identification of elements under selective pressure in multiple sequence alignments of closely related genomes, such as in comparisons of human-to-primate or mouse-to-rat DNA. This tool integrates two different statistical methods and allows for the dynamic visualization of the resulting conservation profile. eShadow also includes a versatile optimization module capable of training the underlying Hidden Markov Model to differentially predict functional sequences. This module grants the tool high flexibility in the analysis of multiple sequence alignments and in comparing sequences with different divergence rates. Here, we describe the eShadow comparative tool and its potential uses for analyzing both multiple nucleotide and protein alignments to predict putative functional elements.
authors.affiliation: Energy, Environment, Biology and Institutional Computing (EEBI), Lawrence Livermore National Laboratory, Livermore, California 94550, USA. ovcharenko1@llnl.gov
authors.forename: Ivan
authors.initials: I
authors.lastname: Ovcharenko
authors.forename: Dario
authors.initials: D
authors.lastname: Boffelli
authors.forename: Gabriela G
authors.initials: GG
authors.lastname: Loots
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D017124:Conserved Sequence / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D030541:Databases, Genetic; D005091:Exons / Q000235:genetics; D006801:Humans; D010215:Papio / Q000235:genetics; D010455:Peptides / Q000235:genetics; D017434:Protein Structure, Tertiary / Q000235:genetics; D011506:Proteins / Q000235:genetics; D012984:Software; D012985:Software Design
chemical_list: D021901:DNA, Intergenic; D010455:Peptides; D011506:Proteins