Data Mining in Bioinformatics

1. Front Matter

   Pages i-xi

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2. Overview

   1. Introduction to Data Mining in Bioinformatics

      • Jason T. L. Wang, Mohammed J. Zaki, Hannu T. T. Toivonen, Dennis Shasha

      Pages 3-8

   2. Survey of Biodata Analysis from a Data Mining Perspective

      • Peter Bajcsy, Jiawei Han, Lei Liu, Jiong Yang

      Pages 9-39

3. Sequence and Structure Alignment

   1. AntiClustAl: Multiple Sequence Alignment by Antipole Clustering

      • Cinzia Di Pietro, Alfredo Ferro, Giuseppe Pigola, Alfredo Pulvirenti, Michele Purrello, Marco Ragusa et al.

      Pages 43-57

   2. RNA Structure Comparison and Alignment

      • Kaizhong Zhang

      Pages 59-81

4. Biological Data Mining

   1. Piecewise Constant Modeling of Sequential Data Using Reversible Jump Markov Chain Monte Carlo

      • Marko Salmenkivi, Heikki Mannila

      Pages 85-103

   2. Gene Mapping by Pattern Discovery

      • Petteri Sevon, Hannu T. T. Toivonen, Päivi Onkamo

      Pages 105-126

   3. Predicting Protein Folding Pathways

      • Mohammed J. Zaki, Vinay Nadimpally, Deb Bardhan, Chris Bystroff

      Pages 127-141

   4. Data Mining Methods for a Systematics of Protein Subcellular Location

      • Kai Huang, Robert F. Murphy

      Pages 143-187

   5. Mining Chemical Compounds

      • Mukund Deshpande, Michihiro Kuramochi, George Karypis

      Pages 189-215

5. Biological Data Management

   1. Phyloinformatics: Toward a Phylogenetic Database

      • Roderic D. M. Page

      Pages 219-241

   2. Declarative and Efficient Querying on Protein Secondary Structures

      • Jignesh M. Patel, Donald P. Huddler, Laurie Hammel

      Pages 243-273

   3. Scalable Index Structures for Biological Data

      • Ambuj K. Singh

      Pages 275-296

6. Back Matter

   Pages 297-340

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8. 1. 1 Protein Subcellular Location The life sciences have entered the post-genome era where the focus of biologicalresearchhasshiftedfromgenomesequencestoproteinfunctionality. Withwhole-genomedraftsofmouseandhumaninhand,scientistsareputting more and more e?ort into obtaining information about the entire proteome in a given cell type. The properties of a protein include its amino acid sequences, its expression levels under various developmental stages and in di?erenttissues,its3Dstructureandactivesites,itsfunctionalandstructural binding partners, and its subcellular location. Protein subcellular location is important for understanding protein function inside the cell. For example, the observation that the product of a gene is localized in mitochondria will support the hypothesis that this protein or gene is involved in energy metabolism. Proteins localized in the cytoskeleton are probably involved in intracellular tra?cking and support. The context of protein functionality is well represented by protein subcellular location. Proteins have various subcellular location patterns [250]. One major category of proteins is synthesized on free ribosomes in the cytoplasm. Soluble proteins remain in the cytoplasm after their synthesis and function as small factories catalyzing cellular metabolites. Other proteins that have a target signal in their sequences are directed to their target organelle (such as mitochondria) via posttranslational transport through the organelle membrane. Nuclear proteins are transferred through pores on the nuclear envelope to the nucleus and mostly function as regulators. The second major category of proteins is synthesized on endoplasmic reticulum(ER)-associated ribosomes and passes through the reticuloendothelial system, consisting of the ERand the Golgi apparatus.

• Alignment
• Markov chain
• XML
• bioinformatics
• biology
• calculus
• classification
• clustering
• computer
• data analysis
• data mining
• database
• microarray
• modeling
• protein
• data structures

• New Jersey Institute of Technology, USA

  Jason T.L. Wang

• Computer Science Department, Rensselaer Polytechnic Institute, USA

  Mohammed J. Zaki

• University of Helsinki and Nokia Research Center, Helsinki

  Hannu T.T. Toivonen

• New York University, USA

  Dennis Shasha

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