ECR Browser :: Details

Applications

ECR Browser features include:     - dynamic conservation profiles     - multiple tracks of gene annotation     - gene expression, SNP, repeat, and other sources of data overlayed on top of conservation     - identification of conserved transcription factor binding sites     - whole genome alignments for user-submitted sequences     - custom genome annotation track     - mouse-wheel zoom in/out, keyboard shortcuts

Alignments

ECR Browser  is based on a series of pairwise genome alignments generated in the following manner:     Step 1. A pair of genomes is downloaded from a genome repository.     Step 2. Homology relationship are established betwees two genomes. In order to do so, we utilize BLAT and BLAST mapping tools.     Step 3. A pair of sequences from every homology block is aligned to establish nucleotide level match-mismatch similarity profiles . We use blastz (Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W., Human-mouse alignments with BLASTZ, Genome Res. 2003 Jan;13(1):103-7.) to align the sequences.

Availability and restrictions of use

ECR Browser is publicly available at http://ecrbrowser.dcode.org/.