CSTminer

CSTminer identifies Conserved Sequence Tags (CST) in genomic sequences through pairwise comparisons to detect statistically significant conserved blocks and assess their coding potential for functional annotation.

Key Features:

• CST detection algorithm: Detects statistically significant conserved blocks across genomes using pairwise sequence comparisons.
• Coding potential scoring: Calculates a coding potential score to distinguish coding versus non-coding conserved blocks.
• Annotation integration: Maps and overlays detected conserved sequences onto Ensembl exons and expressed sequence tags (ESTs).
• Functional interpretation: Relates conserved sequences to coding exons and regulatory motifs.
• Statistical assessment: Provides statistical significance assessments for detected conserved blocks.
• Graphical output: Produces graphical representations that display conserved blocks in the context of Ensembl annotations and ESTs.

Scientific Applications:

• Whole-genome functional annotation: Supports annotation of genomes by identifying conserved elements relevant to function.
• Novel coding region identification: Aids discovery of previously unannotated coding exons via coding potential scoring.
• Regulatory element discovery: Facilitates identification of conserved regulatory motifs across species.
• Evolutionary genomics: Enables study of evolutionary conservation by comparing conserved blocks between genomes.
• Annotation cross-referencing: Allows correlation of conserved blocks with Ensembl exons and EST evidence.

Methodology:

Performs pairwise sequence comparisons, applies an algorithm to detect statistically significant conserved blocks, calculates a coding potential score, overlays detected conserved sequences onto Ensembl exons and expressed sequence tags (ESTs), and returns statistical significance assessments and graphical outputs.