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Molecular Biology Tools
Open Directory - Science: Biology: Bioinformatics: Online Services: Molecular Biology Tools
Science: Biology: Biochemistry and Molecular Biology: Biomolecules: Nucleic Acids
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- Translates a plane format of the DNA sequence (first ORF only) to amino acid sequence. Provides numbering of every 10th AA and every 30th bp and align them by codon.
Graphical Codon Usage Analyzer
- Displays the codon quality in two different ways, codon usage frequency or relative adaptiveness values. FAQ included.
- Generates primers for Ligation Independent Cloning (LIC).
- 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.
- 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.
- 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.
- Provides primers specific to the PCR template sequence. Includes primer pair specificity checking against a selected database.
- Analyses up to three trace files collected on the ABI 3730 and 3730xl DNA sequencers.
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.
- Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others. Maintained by NIH, USA.
- The restriction enzyme database. Maintained by the New England Biolabs, USA.
- Provides restriction enzyme digest analysis of the input DNA sequence. Results are presented graphically as a "virtual gel".
- Finds restriction enzyme cleavage sites in linear and circular DNA sequences. Provides also a virtual digest function.
- Silent mutation restriction enzyme scan. Finds new restriction sites to insert (mutate) with no translation change.
- A Java application that facilitates the identification of potential ORFs, based on provided DNA sequence and probable ORF length.
- 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.
- Provides restriction analysis, silent mutation scanning and SNP-RFLP analysis. Allows for utilization of all commercially available type II restriction enzymes.
- Provides a map of restriction enzyme sites and a list of non-cutting enzymes for a corresponding DNA sequence.
Molecular Biology Tools
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Last update: Tuesday, April 9, 2013 1:33:57 AM EDT -