Nfeature: A platform for computing features of nucleotide sequences

Abstract

In the past few decades, public repositories on nucleotides have increased with exponential rates. This pose a major challenge to researchers to predict the structure and function of nucleotide sequences. In order to annotate function of nucleotide sequences it is important to compute features/attributes for predicting function of these sequences using machine learning techniques. In last two decades, several software/platforms have been developed to elicit a wide range of features for nucleotide sequences. In order to complement the existing methods, here we present a platform named Nfeature developed for computing wide range of features of DNA and RNA sequences. It comprises of three major modules namely Composition, Correlation, and Binary profiles. Composition module allow to compute different type of compositions that includes mono-/di-tri-nucleotide composition, reverse complement composition, pseudo composition. Correlation module allow to compute various type of correlations that includes auto-correlation, cross-correlation, pseudo-correlation. Similarly, binary profile is developed for computing binary profile based on nucleotides, di-nucleotides, di-/tri-nucleotide properties. Nfeature also allow to compute entropy of sequences, repeats in sequences and distribution of nucleotides in sequences. In addition to compute feature in whole sequence, it also allows to compute features from part of sequence like split-composition, N-terminal, C-terminal. In a nutshell, Nfeature amalgamates existing features as well as number of novel features like nucleotide repeat index, distance distribution, entropy, binary profile, and properties. This tool computes a total of 29217 and 14385 features for DNA and RNA sequence, respectively. In order to provide, a highly efficient and user-friendly tool, we have developed a standalone package and web-based platform (https://webs.iiitd.edu.in/raghava/nfeature).