- Search for TFs
- Search for Genes
- Search for Associations
Support & suggestions:
The IUPAC Code Generation utility finds the most compressed representation for a set of DNA strings of the same length, using a degenerate code, that corresponds to the standard nomenclature used by International Union for Pure and Applied Chemistry (IUPAC). This compact representation is based on "multiple-valued logic minimization" approach .
The utility requires a set of sequences of the same length.Back to top
The output is the most compressed representation of the inserted set of DNA sequences. This compaction of is different from the usual probabilistic compaction of aligned DNA sequences that is based on the position specific frequency of bases. Since the IUPAC code generation as implemented in YEASTRACT does not consider probability of occurrence of a base at a particular location, it does not add further information other than the given sequences. Therefore, the compressed code generated in such a way would give the same set of sequences upon decompression, therefore, preserving the original details. The result is usually a smaller set of strings with one or more ambiguous bases, describing concisely, but also precisely, a set of similar or related DNA strings, such as TF binding sites.
IUPAC code generation is an adoption of ESPRESSO tool for multiple-valued logic minimization by Richard Rudell and Alberto Sangiovanni-Vincentelli, done by Nuno Mendes and David Nunes .Back to top
Standard IUPAC Nucleotide code is used to describe ambiguous sites in a given DNA sequence motif, where a single character may represent more than one nucleotide. The code is shown in the table below.
Table adapted from .Back to top
 R. Rudell and A. L. Sangiovanni-Vincentelli. Multiple-Valued
Minimization for PLA Optimization. IEEE Transactions on Computer-Aided
Design, CAD-6:727-750, September 1987. Link
 N. Mendes and D. Nunes, Geração de Código IUPAC, INESC-ID Tec. Rep. 16/2004, Jul 2004. Link
 Biochem J. 229(2): 281–286, July 15 1985. PubMedBack to top
|Back to top|