The Sequence Molecular Analysis Tools module

BioNumerics uses proven technology acquired from the Kodon software to bring various specialized sequence analysis functions. Taking all features of the Sequence Types and the Molecular Analysis Tools together, BioNumerics offers a rich and versatile sequence analysis platform.

Frame analysis
Finds all open reading frames (ORF) and predicts protein coding sequences (PCS) on a sequence. It lists all ORFs and possible PCS regions for all 6 translation frames, for a given translation table and codon usage table. The user can specify an optional ORF and PCS length filter. ORFs and amino acid translations can be plotted on a graphical sequence display.

Restriction enzyme analysis
In-silico multi-purpose analysis of restriction enzyme cleavage suitable for cloning experiments as well as for RFLP, PFGE and AFLP design. Thousands of restriction enzymes from ReBase can be downloaded and stored, and subsets of enzymes of particular interest can be created (e.g. 4-cutters, blunt-cutters, cheap enzymes, available enzymes...). Up to full chromosomes can be analyzed so that optimal enzymes can be selected for electrophoresis-based fragment typing techniques such as PFGE, RFLP and AFLP. Individual enzyme cleavage fragments or combinations of different enzymes can be displayed on pseudo-gel images to predict the results of typing techniques or cloning experiments.

Primer design
Searches for optimal primers or primer combinations for the most diverse experiment setups by taking into account various experimental parameters. The user can specify various primer properties such as preferential length and melting temperature, %GC boundaries, maximal degeneracy, etc. Forward and reverse primers and PCR combinations can be sorted and selected according to different parameters (position, melting temperature, length, degeneracy, %GC...). Selected primer pairs can be stored in the Oligonucleotide database.

In combination with the Tree and Network Inference module, primer design can be launched from the Multiple alignment window to find discriminatory primer pairs between defined groups of sequences. This application is very suitable for the design of PCR detection tests.

Features:

• Frame analysis. Find all open reading frames (ORF) and predict protein coding sequences (PCS) on a sequence.
• Restriction enzyme analysis. In-silico multi-purpose analysis of restriction enzyme cleavage suitable for cloning experiments as well as for RFLP, PFGE and AFLP design.
• Primer design. Search for optimal primers or primer combinations for the most diverse experiment setups by taking into account various experimental parameters. Includes differential primer search to design primers or probes that discriminate selected sets of sequences from each other.

This module can only be used in combination with the Sequence Types Module.