eShadow: A Tool for Comparing Closely Related Sequences

AUTOR(ES)

Ovcharenko, Ivan

FONTE

Cold Spring Harbor Laboratory Press

RESUMO

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.

Documentos Relacionados

• “Shadow” OSCE examiner. A cross-sectional study comparing the “shadow” examiner with the original OSCE examiner format
• Hybrid DNA artifact from PCR of closely related target sequences.
• A statistical test for comparing several nucleotide sequences
• The use of PCR-RFLP as an identification tool for two closely related species of bats of genus Platyrrhinus
• Closely related DNA sequences specify distinct patterns of developmental expression in Drosophila melanogaster.