In this paper we will discuss the benefits and disadvantagesof the current approaches for storing biological sequence information.We have developed a hybrid representation that uses thecompactness of the sequence, together with the detail of chemical connectivityinformation for modified regions. It represents standard residues withsubstructure. All instances of the same residue are represented by a singletemplate. This hybrid approach is compact and scalable.We have developed a converter that takes a UniProt formatfile extracts the sequence information and derives the modifications producingan SCSR record. The SCSR is encoded as a molfile and registered into a SymyxDirect database. Duplicate checking, exact matching � with and without themodifications �molecular weight calculation, and substructure searching are allavailable with these structures.We are using this representation for peptides,oligonucleotides, and we are now extending it to oligosaccharides. Non-naturalresidues can be included in an SCSR.

Self-contained
sequence representation (SCSR): Bridging the gap between bioinformatics and
cheminformatics

240th National Meeting (2010)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.

Self-contained sequence representation (SCSR): Bridging the gap between bioinformatics and cheminformatics