Directory of Molecular Biology Tools Resources

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

Resources in This Category

• Graphical Codon Usage Analyzer

  http://gcua.schoedl.de/
  Displays the codon quality in two different ways, codon usage frequency or relative adaptiveness values. FAQ included.

• NEBcutter

  http://tools.neb.com/NEBcutter2/
  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

  http://www.basic.northwestern.edu/biotools/OligoCalc.html
  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

  http://www.ncbi.nlm.nih.gov/gorf/gorf.html
  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

  http://wishart.biology.ualberta.ca/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

  http://www.ncbi.nlm.nih.gov/tools/primer-blast/
  Provides primers specific to the PCR template sequence. Includes primer pair specificity checking against a selected database.

• RaCC: Rare Codon Calculator

  http://nihserver.mbi.ucla.edu/RACC/
  Determines the number and highlights a rare E. coli codons in a provided DNA sequence. Maintained by UCLA, USA.

• Rare Codon Analysis

  http://www.genscript.com/cgi-bin/tools/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

  http://www-bimas.cit.nih.gov/molbio/readseq/
  Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others. Maintained by NIH, USA.

• REBASE

  http://rebase.neb.com/rebase/rebase.html
  The restriction enzyme database. Maintained by the New England Biolabs, USA.

• REBsites

  http://tools.neb.com/REBsites/
  Provides restriction enzyme digest analysis of the input DNA sequence. Results are presented graphically as a "virtual gel".

• RestrictionMapper

  http://www.restrictionmapper.org/
  Finds restriction enzyme cleavage sites in linear and circular DNA sequences. Provides also a virtual digest function.

• Silent

  http://mobyle.pasteur.fr/cgi-bin/portal.py?form=silent
  Silent mutation restriction enzyme scan. Finds new restriction sites to insert (mutate) with no translation change.

• StarORF

  http://web.mit.edu/star/orf/
  A Java application that facilitates the identification of potential ORFs, based on provided DNA sequence and probable ORF length.

• TACG

  http://mobyle.pasteur.fr/cgi-bin/portal.py?form=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

  http://watcut.uwaterloo.ca/watcut/watcut/template.php
  Provides restriction analysis, silent mutation scanning and SNP-RFLP analysis. Allows for utilization of all commercially available type II restriction enzymes.

Related Categories

• Home > Science > Biology > Biochemistry and Molecular Biology > Methods and Techniques
• Home > Science > Biology > Biochemistry and Molecular Biology > Products and Services
• Home > Science > Biology > Biochemistry and Molecular Biology > Biomolecules > Nucleic Acids

 

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