Comparing nucleotide and protein sequences by linguistic methods.
Nucleotide and amino acid sequences can be analyzed and compared by their oligomer compositions. Such methods are fundamentally different from comparison methods based on sequence alignment. They are analogous to the linguistic analysis of human texts. The methods have a wide range of sensitivity and can identify homologous as well as functionally and taxonomically related sequences. Significant sequence dissimilarity can also be identified enabling detection of foreign DNA sequences in genomes, genetic libraries and databases. The simplicity and speed of linguistic methods make them very suitable for database searching and maintenance and as a preliminary step to more specific and time-consuming analysis methods.
Pietrokovski
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Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D001709:Biotechnology; D004271:DNA, Fungal / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D006801:Humans; D008037:Linguistics; D051379:Mice; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D051381:Rats; D012190:Retroviridae / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017386:Sequence Homology, Amino Acid
D004271:DNA, Fungal; D004272:DNA, Mitochondrial; D004279:DNA, Viral