In silico simulation of molbio experiments

In silico simulation of molbio experiments simulates molecular biology experiments on completely sequenced bacterial genomes to predict PCR and AFLP fragment sizes and sequences, map restriction sites, generate PFGE banding simulations, and identify ORFs and translated proteins.

Key Features:

• Genome Database: Supports analysis of over 300 complete bacterial genomes and their associated plasmids.
• In Silico PCR Amplification: Simulates PCR using user-specified primers on selected genomes and reports fragment sizes, nucleotide sequences, and corresponding ORFs.
• AFLP-PCR Analysis: Performs theoretical AFLP-PCR experiments, analyzes fragment sizes and sequences, and suggests commercial restriction enzyme pairs capable of generating up to 50 amplicons.
• Endonuclease Restriction Analysis: Calculates numbers and locations of restriction sites for various endonucleases within genomes and plasmids and reports resulting fragment sets.
• PFGE and Restriction Map Generation: Produces PFGE images and restriction maps for fragment sets of 50 or fewer fragments.
• ORF Search by Name: Locates open reading frames within genomes by name.
• DNA to Protein Translation: Translates nucleotide sequences into corresponding protein sequences.
• User-Defined Restriction Digestion: Performs restriction analysis on user-supplied DNA sequences.

Scientific Applications:

• Primer design and validation: Predicts PCR product sizes and sequences for in silico validation of primer sets and target ORFs.
• AFLP experiment planning: Models AFLP-PCR fragment patterns and supports selection of restriction enzyme pairs to achieve targeted amplicon counts.
• Restriction mapping and typing: Anticipates restriction fragment distributions and PFGE banding patterns for comparative genomics and molecular typing.
• Annotation and translation: Identifies ORFs and provides nucleotide-to-protein translations to support functional genomics analyses.

Methodology:

Computational methods explicitly include in silico PCR amplification, AFLP-PCR simulation, endonuclease restriction site counting, fragment size and sequence reporting, PFGE image generation, restriction map construction, ORF identification by name, DNA-to-protein translation, user-defined restriction digestion, and an enzyme-pair suggestion function that recommends commercial restriction enzyme pairs yielding up to 50 amplicons.