WebMAM

WebMAM processes multiple sequence alignments to identify exons, common repeat elements, and unique regions, extract subalignments for targeted analyses, and generate graphical summaries to support phylogenetic and comparative genomic studies.

Key Features:

• Identification of Genomic Regions: Computes precise locations of exons, common repeat elements, and unique regions within multiple sequence alignments using user-specified programs, databases, or tables.
• Subalignment Extraction: Extracts subalignments corresponding to specified DNA regions for independent or combined analyses.
• Graphical Display and Sequence Variation Assessment: Generates graphical displays to assess sequence variation with separate visualizations for repeat, non-repeat, and coding portions of genomic DNA.
• Facilitation of Phylogenetic Analysis: Processes distinct portions of genomic sequences to support phylogenetic and comparative genomic analyses in large-scale sequencing projects.

Scientific Applications:

• Genomic Research: Investigation of genome structural organization with focus on coding and non-coding regions using aligned sequence data.
• Evolutionary Studies: Phylogenetic analysis by comparing genomic variations across species or populations.
• Functional Genomics: Identification of exons and repeat elements to inform studies of gene function and regulation.

Methodology:

Uses user-specified programs, databases, or tables to identify genomic features from multiple alignments, extracts subalignments for targeted regions, and produces graphical representations of sequence variation.