title: ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.
abstract: With an increasing number of vertebrate genomes being sequenced in draft or finished form, unique opportunities for decoding the language of DNA sequence through comparative genome alignments have arisen. However, novel tools and strategies are required to accommodate this large volume of genomic information and to facilitate the transfer of predictions generated by comparative sequence alignment to researchers focused on experimental annotation of genome function. Here, we present the ECR Browser, a tool that provides easy and dynamic access to whole genome alignments of human, mouse, rat and fish sequences. This web-based tool (http://ecrbrowser.dcode.org) provides the starting point for discovery of novel genes, identification of distant gene regulatory elements and prediction of transcription factor binding sites. The genome alignment portal of the ECR Browser also permits fast and automated alignments of any user-submitted sequence to the genome of choice. The interconnection of the ECR Browser with other DNA sequence analysis tools creates a unique portal for studying and exploring vertebrate genomes.
authors.affiliation: Genome Biology Division and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA. ovcharenko1@llnl.gov
authors.forename: Ivan
authors.initials: I
authors.lastname: Ovcharenko
authors.forename: Marcelo A
authors.initials: MA
authors.lastname: Nobrega
authors.forename: Gabriela G
authors.initials: GG
authors.lastname: Loots
authors.forename: Lisa
authors.initials: L
authors.lastname: Stubbs
mesh_terms: D000818:Animals; D001665:Binding Sites; D003196:Computer Graphics; D005399:Fishes / Q000235:genetics; D016678:Genome; D023281:Genomics; D006801:Humans; D020407:Internet; D051379:Mice; D051381:Rats; D012045:Regulatory Sequences, Nucleic Acid; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software; D026801:Synteny; D018511:Systems Integration; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors