INFLUENZA A VIRUS (H3N2) GENOMIC SEQUENCE DIFFERENCE MEASURES BASED ON WORD ABSENCE and EXPRESSION LEVELS

摘要

In a genomic sequence, the oligonucleotide signature represents the ratio of the observed to expected number of occurrences of all possible nucleotide words of a specific length. Word absence is also found in genomic sequences whereby specific words are not observed despite their expected presence in a random nucleotide distribution. This research uses a combination of word absence and oligonucleotide signatures to quantify differences between inter-epidemic and intra-epidemic Influenza A virus (H3N2) genomic sequences. In addition, word absence/presence patterns are examined for their discrimination of sequences from distinct epidemics or geographic origins within the same epidemic. Inter-epidemic sequences are well delineated by word absences and difference measures into epidemic specific groups. Intra-epidemic sequences are not consistently well separable in terms of their geographic origins, but show similarities across geographic regions.