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Computational Intelligence and Pattern Analysis in Biological Informatics by Jason T. Wang, Sanghamitra Bandyopadhyay, Ujjwal Maulik

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CHAPTER 3

BIOLOGICAL INFORMATICS: DATA, TOOLS, AND APPLICATIONS

KEVIN BYRON, MIGUEL CERVANTES-CERVANTES, AND JASON T. L. WANG

3.1 INTRODUCTION

Biological informatics (BI) has emerged as one of the most important interdisciplinary fields in the last decade. Major research efforts in BI include nucleotide sequence and structure alignment, gene finding and genome assembly, gene expression and regulation, protein and ribonucleic acid (RNA) structure prediction, biological networks and pathway analysis, genome-wide association studies, computational proteomics and biomarker detection, molecular evolution and population genetics, to name a few. These efforts are often concurrent with the development of software tools for data analysis, leading to new discoveries in diverse areas of the biological sciences

This chapter presents a case study in BI, focusing on locating noncoding RNAs (ncRNAs) in Drosophila genomes using software tools, in particular the Infernal package Noncoding RNAs are functional RNA transcripts that are not messenger RNAs (mRNAs) and therefore are not templates in protein biosynthesis. Recent experiments have shown that ncRNAs perform a wide range of cellular functions [8]. In particular, RNA on the X-1 (roX1) plays an essential role in the dosage compensation system, which increases the transcription level on the X chromosome in Drosophila males (XY) with respect to that of females (XX) [9]. Experiments have shown roX1 functionality in some species of Drosophila ...

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