Similarity search and analysis of protein sequences and structures: a residue contacts based approach

Download

index.pdf

Date

2008

Author

Saçan, Ahmet

Metadata

Show full item record

Item Usage Stats

159
views

53
downloads

The advent of high-throughput sequencing and structure determination techniques has had a tremendous impact on our quest in cracking the language of life. The genomic and protein data is now being accumulated at a phenomenal rate, with the motivation of deriving insights into the function, mechanism, and evolution of the biomolecules, through analysis of their similarities, differences, and interactions. The rapid increase in the size of the biomolecular databases, however, calls for development of new computational methods for sensitive and efficient management and analysis of this information. In this thesis, we propose and implement several approaches for accurate and highly efficient comparison and retrieval of protein sequences and structures. The observation that corresponding residues in related proteins share similar inter-residue contacts is exploited in derivation of a new set of biologically sensitive metric amino acid substitution matrices, yielding accurate alignment and comparison of proteins. The metricity of these matrices has allowed efficient indexing and retrieval of both protein sequences and structures. A landmark-guided embedding of protein sequences is developed to represent subsequences in a vector space for approximate, but extremely fast spatial indexing and similarity search. Whereas protein structure comparison and search tasks were hitherto handled separately, we propose an integrated approach that serves both of these tasks and performs comparable to or better than other available methods. Our approach hinges on identification of similar residue contacts using distance-based indexing and provides the best of the both worlds: the accuracy of detailed structure alignment algorithms, at a speed comparable to that of the structure retrieval algorithms. We expect that the methods and tools developed in this study will find use in a wide range of application areas including annotation of new proteins, discovery of functional motifs, discerning evolutionary relationships among genes and species, and drug design and targeting.

Subject Keywords

Computer software., Research

URI

http://etd.lib.metu.edu.tr/upload/12609754/index.pdf
https://hdl.handle.net/11511/17830

Collections

Graduate School of Natural and Applied Sciences, Thesis

Suggestions

OpenMETU
Core

Coupling speech recognition and rule-based machine translation Köprü, Selçuk; Yazıcı, Adnan; Department of Computer Engineering (2008) The objective of this thesis was to study the coupling of automatic speech recognition (ASR) systems with rule-based machine translation (MT) systems. In this thesis, a unique approach to integrating ASR with MT for speech translation (ST) tasks was proposed. The proposed approach is unique, essentially because it includes the rst rule-based MT system that can process speech data in a word graph format. Compared to other rule-based MT systems, our system processes both a word graph and a stream of words. Th...
Expert finding in domains with unclear topics Selçuk Doğan, Gonca Hülya; Taşkaya Temizel, Tuğba; Department of Information Systems (2012) Expert finding is an Information Retrieval (IR) task that is used to find the needed experts. To find the needed experts is a noticeable problem in many commercial, educational or governmental organizations. It is highly crucial to find the appropriate experts, when seeking referees for a paper submitted to a conference or when looking for a consultant for a software project. It is also important to find the similar experts in case of the absence or the inability of the selected expert. Traditional expert f...
A systematic study of probabilistic aggregation strategies in swarm robotic systems Soysal, Onur; Şahin, Erol; Department of Computer Engineering (2005) In this study, a systematic analysis of probabilistic aggregation strategies in swarm robotic systems is presented. A generic aggregation behavior is proposed as a combination of four basic behaviors: obstacle avoidance, approach, repel, and wait. The latter three basic behaviors are combined using a three-state finite state machine with two probabilistic transitions among them. Two different metrics were used to compare performance of strategies. Through systematic experiments, how the aggregation performa...
Subsequence feature maps for protein function annotation Saraç, Ömer Sinan; Atalay, Mehmet Volkan; Department of Computer Engineering (2008) With the advances in sequencing technologies, the number of protein sequences with unknown function increases rapidly. Hence, computational methods for functional annotation of these protein sequences become of the upmost importance. In this thesis, we first defined a feature space mapping of protein primary sequences to fixed dimensional numerical vectors. This mapping, which is called the Subsequence Profile Map (SPMap), takes into account the models of the subsequences of protein sequences. The resulting...
Free gait generation with reinforcement learning for a six-legged robot Erden, Mustafa Suphi; Leblebicioğlu, Mehmet Kemal (Elsevier BV, 2008-03-31) In this paper the problem of free gait generation and adaptability with reinforcement learning are addressed for a six-legged robot. Using the developed free gait generation algorithm the robot maintains to generate stable gaits according to the commanded velocity. The reinforcement learning scheme incorporated into the free gait generation makes the robot choose more stable states and develop a continuous walking pattern with a larger average stability margin. While walking in normal conditions with no ext...

Citation Formats

A. Saçan, “Similarity search and analysis of protein sequences and structures: a residue contacts based approach,” Ph.D. - Doctoral Program, Middle East Technical University, 2008.