This category is for bioinformatics tools that aid the preparation or analysis of molecular biology methods.

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Graphical Codon Usage Analyzer
Displays the codon quality in two different ways, codon usage frequency or relative adaptiveness values. FAQ included.
NEBcutter
Provides a DNA sequence analysis to find restriction enzymes sites. Finds also non-overlapping open reading frames using the E.coli genetic code.
Oligo Calc: Oligonucleotide Properties Calculator
Provides reverse complement sequence for DNA or RNA primer strands, self complementarity check, physical and thermodynamic constants, melting temperature (Tm). Includes calculation formulas.
ORF Finder
Identifies all ORFs using the standard or alternative genetic codes. Provides an interactive, graphical interface and allow for saving of a deduced amino acid sequence in various formats. Allows searching against the sequence database using the BLAST server.
PlasMapper
Offers server generated plasmid maps and image files, from input DNA sequences up to 20,000 bp. Includes citation, and downloadable source code. Maintained by the University of Alberta, USA.
Primer-BLAST
Provides primers specific to the PCR template sequence. Includes primer pair specificity checking against a selected database.
RaCC: Rare Codon Calculator
Determines the number and highlights a rare E. coli codons in a provided DNA sequence. Maintained by UCLA, USA.
Rare Codon Analysis
Provides graphical and numerical representation of the codon adaptation index, frequency distribution and GC content of the DNA sequence. Maintained by the GenScript, USA.
Readseq
Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others. Maintained by NIH, USA.
REBASE
The restriction enzyme database. Maintained by the New England Biolabs, USA.
REBsites
Provides restriction enzyme digest analysis of the input DNA sequence. Results are presented graphically as a "virtual gel".
RestrictionMapper
Finds restriction enzyme cleavage sites in linear and circular DNA sequences. Provides also a virtual digest function.
Silent
Silent mutation restriction enzyme scan. Finds new restriction sites to insert (mutate) with no translation change.
StarORF
A Java application that facilitates the identification of potential ORFs, based on provided DNA sequence and probable ORF length.
TACG
DNA restriction enzyme analysis. Provides a number of hits per enzyme and a list of non-cutters. Allows for selection of the enzymes and parameters.
WatCut
Provides restriction analysis, silent mutation scanning and SNP-RFLP analysis. Allows for utilization of all commercially available type II restriction enzymes.
[Computer Mozilla]
Last update:
September 2, 2015 at 7:45:07 UTC
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