zPicture: dynamic alignment and visualization tool for analyzing conservation profiles.
Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, an interactive Web-based sequence alignment and visualization tool for dynamically generating conservation profiles and identifying evolutionarily conserved regions (ECRs). zPicture is highly flexible, because critical parameters can be modified interactively, allowing users to differentially predict ECRs in comparisons of sequences of different phylogenetic distances and evolutionary rates. We demonstrate the application of this module to identify a known regulatory element in the HOXD locus, in which functional ECRs are difficult to discern against the highly conserved genomic background. zPicture also facilitates transcription factor binding-site analysis via the rVista tool portal. We present an example of the HBB complex when zPicture/rVista combination specifically pinpoints to two ECRs containing GATA-1, NF-E2, and TAL1/E47 binding sites that were identified previously as transcriptional enhancers. In addition, zPicture is linked to the UCSC Genome Browser, allowing users to automatically extract sequences and gene annotations for any recorded locus. Finally, we describe how this tool can be efficiently applied to the analysis of nonvertebrate genomes, including those of microbial organisms.
Ovcharenko
Ivan
I
Energy, Environment, Biology and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA.
Loots
Gabriela G
GG
Hardison
Ross C
RC
Miller
Webb
W
Stubbs
Lisa
L
D000818:Animals; D001665:Binding Sites / Q000235:genetics; D003196:Computer Graphics; D017124:Conserved Sequence / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D006801:Humans; D051379:Mice; D009166:Mycobacterium leprae / Q000235:genetics; D009169:Mycobacterium tuberculosis / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D014157:Transcription Factors / Q000235:genetics
D004269:DNA, Bacterial; D014157:Transcription Factors