DNA fragment assembly using neural prediction techniques.

Abstract

The paper describes an alternative approach to the fragment assembly problem. The key idea is to train a recurrent neural network to tracking the sequence of bases constituting a given fragment and to assign to a same cluster all the sequences which are well tracked by this network. We make use of a 3-layer Recurrent Perceptron and examine both edited sequences from a ftp site and artificial fragments from a common simulation software: the clusters we obtain exhibit interesting properties in terms of error filtering, stability and self consistency; we define as well, with a certain degree of approximation, a metric on the fragment set. The proposed assembly algorithm is susceptible to becoming an alternative method with the following properties: (i) high quality of the rebuilt genomic sequences, (ii) high parallelizability of the computing process with consequent drastic reduction of the running time.