Mapping of the Genome Sequence Using Two-stage Self Organizing Maps

Abstract

In this paper, we introduce an algorithm of Self-Organizing Maps(SOM) which can map the genome sequence continuously on the map. The DNA sequences are considered to have the special features depending on the regions where the sequences are taken from or the gene functions of the proteins which are translated from the sequences. If the hidden features of the DNA sequences are extracted from the DNA sequences, they can be used for predicting the regions or the functions of the sequences. In this paper, we propose the algorithms using two stage SOM which organizes the sequences of the specific length at the first stage and organizes the set of sequences at the 2nd stage This algorithm can map the genome sequences on the map at each stage depending on the features of the sequences. We made some analyses of the genome sequences concerning the functions, species and secondary structure of the sequences.