This category is for bioinformatics tools that aid the preparation or analysis of molecular biology methods.
Related categories 3
Sites 16
- REBASE The restriction enzyme database. Maintained by the New England Biolabs, USA.
- WatCut Provides restriction analysis, silent mutation scanning and SNP-RFLP analysis. Allows for utilization of all commercially available type II restriction enzymes.
- RestrictionMapper Finds restriction enzyme cleavage sites in linear and circular DNA sequences. Provides also a virtual digest function.
- Graphical Codon Usage Analyzer Displays the codon quality in two different ways, codon usage frequency or relative adaptiveness values. FAQ included.
- 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.
- NEBcutter Provides a DNA sequence analysis to find restriction enzymes sites. Finds also non-overlapping open reading frames using the E.coli genetic code.
- Readseq Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others. Maintained by NIH, USA.
- 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.
- Primer-BLAST Provides primers specific to the PCR template sequence. Includes primer pair specificity checking against a selected database.
- StarORF A Java application that facilitates the identification of potential ORFs, based on provided DNA sequence and probable ORF length.
- 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.
- REBsites Provides restriction enzyme digest analysis of the input DNA sequence. Results are presented graphically as a "virtual gel".
- 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.
- Silent Silent mutation restriction enzyme scan. Finds new restriction sites to insert (mutate) with no translation change.
- 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.