Wise2DBA (EBI)

Wise2DBA (EBI) aligns two genomic sequences by identifying colinear conserved blocks separated by gaps to analyze conservation in noncoding regions.

Key Features:

• DNA Block Aligner (DBA) algorithm: Employs the DBA algorithm to identify colinear conserved blocks flanked by nonconserved sequences that vary in length.
• Noncoding-sequence focus: Specifically tailored to align and analyze noncoding genomic regions subject to genetic drift between species.
• Two-sequence alignment: Performs pairwise alignment of two sequences with emphasis on detecting conserved blocks separated by gaps.
• Conservation analysis dataset: Applied to a dataset of 77 genomic mouse/human gene pairs sourced from the EMBL nucleotide database.
• Conservation metrics: Reports coverage by conserved blocks (>60% identical) in upstream regions (36% overall; up to 70% in the first 100 bp upstream of the transcription start site), 5' UTRs (50%), introns (23%), and 3' UTRs (56%).
• Distribution characterization: Identifies the distribution of conserved blocks across noncoding features, including higher concentration near transcription start sites.

Scientific Applications:

• Comparative genomics: Analysis of noncoding DNA conservation between species, exemplified by mouse versus human comparisons.
• Functional element inference: Identification of conserved noncoding blocks to support inference of candidate regulatory or functional elements.
• Evolutionary analysis: Investigation of the effects of genetic drift on noncoding sequence conservation.
• Large-scale genomic analyses: Applied to datasets of multiple gene pairs for broad comparative studies.

Methodology:

Uses the DNA Block Aligner (DBA) algorithm to detect colinear conserved blocks separated by gaps and flanked by nonconserved sequences; applied to 77 mouse/human genomic gene pairs from the EMBL nucleotide database.