Hexanucleotide frequency database.

Abstract

A database of the frequency of hexanucleotid es observed in different categories of the EMBL public domain sequence database is described. A wide range of procedures in molecular biology could benefit from knowledge of the real, as opposed to the projected, frequency of oligonucleotides in the target genomic DNA or mRNA population. These include the design of primers and probes, the detection of reading frames and other genetic features. It is well known that the frequency n-mers are not equally represented in genomic DNA, or in mRNA derived from it (e.g. Claverie et al, 1986; Arnold et al, 1988; Nussinov, 1991; Bains, 1994). The availablility of relatively large amounts of sequence information has enabled me to produce a table of the hexanucleotide frequencies that are actually found in the sequenced examples of specific gene types and genetic elements.