Web Directory

» DNA translator
   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.
   http://www.dnatoprotein.com

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

» LIC Generator
   Generates primers for Ligation Independent Cloning (LIC).
   http://noxtoolbox.ibs.fr/LICgenerator/

» NEBcutter
   Provides a DNA sequence analysis to find restriction enzymes sites. Finds also non-overlapping open reading frames using the E.coli genetic code.
   http://tools.neb.com/NEBcutter2/

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

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

» PlasMapper
   Offers server generated plasmid maps and image files, from input DNA sequences up to 20,000 bp. Includes citation, and dowloadable source code. Maintained by the University of Alberta, USA.
   http://wishart.biology.ualberta.ca/PlasMapper/

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

» QualTrace Online
   Analyses up to three trace files collected on the ABI 3730 and 3730xl DNA sequencers.
   http://www.nucleics.com/qualtrace-dna-sequencing-demo/

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

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

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

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

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

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

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

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

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

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

» Web Primer
   Allows for automatic primer design for the sequencing or PCR from the DNA template sequence or locus name. Provides a list of pairs of primers with corresponding melting temperature (Tm) and GC content.
   http://seq.yeastgenome.org/cgi-bin/SGD/web-primer

» Webcutter 2.0
   Provides a map of restriction enzyme sites and a list of non-cutting enzymes for a corresponding DNA sequence.
   http://users.unimi.it/~camelot/tools/cut2.html