PlasMapper 3.0

PlasMapper 3.0 annotates and visualizes plasmid sequences to identify and label plasmid features for plasmid design and genetic engineering.

Key Features:

• PlasMapDB: Contains over 2000 pre-annotated plasmids and is searchable by plasmid name, sequence features, restriction sites, preferred host organisms, and sequence length.
• Input support: Accepts plasmid sequences and plasmid maps from PlasMapDB as input for analysis and annotation.
• Annotation capabilities: Annotates promoters, terminators, regulatory sequences, replication origins, selectable markers, and other features commonly found in cloning plasmids.
• Sequence analysis and editing: Supports gene insertion, restriction-site modification, codon optimization, and editing of annotated features, with conversion between circular and linear sequence representations.
• Restriction site analysis: Identifies and enables modification of restriction sites within plasmid sequences.
• Map generation: Generates full-color plasmid maps and textual displays and produces circular and linear plasmid representations in multiple output formats.

Scientific Applications:

• Gene cloning design: Supports planning and designing of gene cloning constructs by annotating cloning-relevant features and restriction sites.
• Expression optimization: Provides codon optimization and host-organism-aware sequence adjustments to support expression of coding sequences in selected hosts.
• Plasmid design and genetic engineering: Applicable to basic plasmid design and to complex genetic engineering projects in academic and commercial biotechnology settings.

Methodology:

Integrates sequence data input, database searching against PlasMapDB, annotation using a feature database, codon optimization, restriction-site identification and modification, and generation of circular and linear plasmid maps and textual displays.