BioNumerics
Sequence Molecular Analysis Tools Module
For an overview see
BioNumerics.
Frame analysis:
finds all open reading frames (ORF) and predicts protein coding
sequences (PCS) on a sequence:
- List all ORFs and possible PCS regions for all 6 translation
frames and specify an optional ORF and PCS length filter.
- Select translation table and codon usage table.
- Plot ORFs and AA translations on 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:
- Download
and store thousands of restriction enzymes from ReBase, and create
subsets of enzymes of particular interest (4-cutters, blunt-cutters,
cheap enzymes, available...).
- 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 application includes multiplex primer design by
calculating optimal sets of compatible primers to amplify multiple
target regions simultaneously.
- Specify various primer properties such as preferential length and
melting temperature, %GC boundaries boundaries, maximal degeneracy,
etc.
- Sort and select forward and reverse primers and PCR
combinations according to different parameters (position, melting
temperature, length, degeneracy, %GC...).
- Store selected primer pairs in the Oligonucleotide
database.
- Start primer design 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.
For further details please download
the BioNumerics/GelCompar pdf brochure.
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