Poster Sessions

GENO -12

Amarendra Yavatkar

A. Yavatkar, Y. Lin, J. Ross, Y. Fann, T. Brody, W. Odenwald

EvoPrinterHD: Comparative Genomics Tool for Rapid Detection and Curation of conserved DNA

Multi-genome comparative analysis has yielded important insights into the molecular details of gene regulation. We present here EvoPrinterHD, a fast, high-resolution comparative genomics tool that automatically generates an uninterrupted species-centric view of sequence conservation and enables the discovery of conserved sequences within rearranged DNA. Currently EvoPrinterHD is available for 5 nematode, 3 mosquito, 12 Drosophila, 25 vertebrate, 17 Staphylococcus, 20 Streptococcus and 22 enteric bacteria genomes. EvoPrinterHD employs a modified BLAT algorithm [enhanced-BLAT (eBLAT)], which detects up to 75% more conserved bases than identified by the BLAT alignments used in the earlier EvoPrinter program. The new program also identifies conserved sequences within rearranged DNA, highlights repetitive DNA, and detects sequencing gaps. EvoPrinterHD currently holds over 112 billion bp of indexed genomes in memory and has the flexibility of selecting a subset of genomes for analysis. An EvoDifferences profile is also generated to portray conserved sequences that are uniquely lost in any one of the orthologs. Finally, EvoPrinterHD incorporates options that allow for (1) re-initiation of the analysis using a different genome\'s aligning region as the reference DNA to detect species-specific changes in less-conserved regions, (2) rapid extraction and curation of conserved sequences, and (3) for bacteria, identifies unique or uniquely shared sequences present in subsets of genomes.