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Nucleic Acids Research, 1992, Vol. 20, No. 6 1405-1410
© 1992

MOLECULAR BIOLOGY

Numerical classification of coding sequences

David W. Collins, Chia-Chang Liu and Thomas H. Jukes

Space Sciences Laboratory and Department of Integrative Biology, University of California Berkeley, CA 94720, USA

Received September 10, 1991. Revised February 14, 1992. Accepted February 14, 1992.

DNA sequences coding for protein may be represented by counts of nucleotides or codons. A complete reading frame may be abbreviated by its base count, e.g. A76C158G121T74 or with the corresponding codon table, e.g. (AAA)o(AAC)1(AAG)9 ...(TTT)o. We propose that these numerical designations be used to augment current methods of sequence annotation. Because base counts and codon tables do not require revision as knowledge of function evolves, they are well-suited to act as cross-references, for example to identify redundant GenBank entries. These descriptors may be compared, in place of DNA sequences, to extract homologous genes from large databases. This approach permits rapid searching with good selectivity.


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