LEADER 05421nam 2200661 a 450 001 9910139396103321 005 20200228053435.0 010 $a1-282-93963-7 010 $a9786612939631 010 $a0-470-89209-9 010 $a0-470-89210-2 035 $a(CKB)2480000000008391 035 $a(EBL)698862 035 $a(SSID)ssj0000466837 035 $a(PQKBManifestationID)11293080 035 $a(PQKBTitleCode)TC0000466837 035 $a(PQKBWorkID)10466607 035 $a(PQKB)10770091 035 $a(MiAaPQ)EBC698862 035 $a(WaSeSS)IndRDA00019615 035 $a(PPN)190203986 035 $a(OCoLC)701308667 035 $a(CaSebORM)9781118101988 035 $a(EXLCZ)992480000000008391 100 $a20110308d2011 uy 0 101 0 $aeng 135 $aur|n|---||||| 181 $ctxt 182 $cc 183 $acr 200 00$aAlgorithms in computational molecular biology$b[electronic resource] $etechniques, approaches and applications /$fedited by Mourad Elloumi, Albert Y. Zomaya 210 1$aHoboken, New Jersey :$cJohn Wiley & Sons,$d2011. 215 $a1 online resource (1085 p.) 225 1 $aWiley series on bioinformatics 300 $aDescription based upon print version of record. 311 $a1-118-10198-7 311 $a0-470-50519-2 320 $aIncludes bibliographical references and index. 327 $aALGORITHMS INCOMPUTATIONALMOLECULAR BIOLOGY; CONTENTS; PREFACE; CONTRIBUTORS; I STRINGS PROCESSING AND APPLICATION TO BIOLOGICAL SEQUENCES; 1 STRING DATA STRUCTURES FOR COMPUTATIONAL MOLECULAR BIOLOGY; 1.1 Introduction; 1.2 Main String Indexing Data Structures; 1.2.1 Suffix Trees; 1.2.2 Suffix Arrays; 1.3 Index Structures for Weighted Strings; 1.4 Index Structures for Indeterminate Strings; 1.5 String Data Structures in Memory Hierarchies; 1.6 Conclusions; References; 2 EFFICIENT RESTRICTED-CASE ALGORITHMS FOR PROBLEMS IN COMPUTATIONAL BIOLOGY; 2.1 The Need for Special Cases 327 $a2.2 Assessing Efficient Solvability Options for General Problems and Special Cases2.3 String and Sequence Problems; 2.4 Shortest Common Superstring; 2.4.1 Solving the General Problem; 2.4.2 Special Case: SCSt for Short Strings Over Small Alphabets; 2.4.3 Discussion; 2.5 Longest Common Subsequence; 2.5.1 Solving the General Problem; 2.5.2 Special Case: LCS of Similar Sequences; 2.5.3 Special Case: LCS Under Symbol-Occurrence Restrictions; 2.5.4 Discussion; 2.6 Common Approximate Substring; 2.6.1 Solving the General Problem; 2.6.2 Special Case: Common Approximate String; 2.6.3 Discussion 327 $a2.7 ConclusionReferences; 3 FINITE AUTOMATA IN PATTERN MATCHING; 3.1 Introduction; 3.1.1 Preliminaries; 3.2 Direct Use of DFA in Stringology; 3.2.1 Forward Automata; 3.2.2 Degenerate Strings; 3.2.3 Indexing Automata; 3.2.4 Filtering Automata; 3.2.5 Backward Automata; 3.2.6 Automata with Fail Function; 3.3 NFA Simulation; 3.3.1 Basic Simulation Method; 3.3.2 Bit Parallelism; 3.3.3 Dynamic Programming; 3.3.4 Basic Simulation Method with Deterministic State Cache; 3.4 Finite Automaton as Model of Computation; 3.5 Finite Automata Composition; 3.6 Summary; References 327 $a4 NEW DEVELOPMENTS IN PROCESSING OF DEGENERATE SEQUENCES4.1 Introduction; 4.1.1 Degenerate Primer Design Problem; 4.2 Background; 4.3 Basic Definitions; 4.4 Repetitive Structures in Degenerate Strings; 4.4.1 Using the Masking Technique; 4.4.2 Computing the Smallest Cover of the Degenerate String x; 4.4.3 Computing Maximal Local Covers of x; 4.4.4 Computing All Covers of x; 4.4.5 Computing the Seeds of x; 4.5 Conservative String Covering in Degenerate Strings; 4.5.1 Finding Constrained Pattern p in Degenerate String T; 4.5.2 Computing ?-Conservative Covers of Degenerate Strings 327 $a4.5.3 Computing ?-Conservative Seeds of Degenerate Strings4.6 Conclusion; References; 5 EXACT SEARCH ALGORITHMS FOR BIOLOGICAL SEQUENCES; 5.1 Introduction; 5.2 Single Pattern Matching Algorithms; 5.2.1 Algorithms for DNA Sequences; 5.2.2 Algorithms for Amino Acids; 5.3 Algorithms for Multiple Patterns; 5.3.1 Trie-Based Algorithms; 5.3.2 Filtering Algorithms; 5.3.3 Other Algorithms; 5.4 Application of Exact Set Pattern Matching for Read Mapping; 5.4.1 MPSCAN: An Efficient Exact Set Pattern Matching Tool for DNA/RNA Sequences; 5.4.2 Other Solutions for Mapping Reads 327 $a5.4.3 Comparison of Mapping Solutions 330 $aThis book represents the most comprehensive and up-to-date collection of information on the topic of computational molecular biology. Bringing the most recent research into the forefront of discussion, Algorithms in Computational Molecular Biology studies the most important and useful algorithms currently being used in the field, and provides related problems. It also succeeds where other titles have failed, in offering a wide range of information from the introductory fundamentals right up to the latest, most advanced levels of study. 410 0$aWiley series on bioinformatics. 606 $aBiophysics$xMathematical models 615 0$aBiophysics$xMathematical models. 676 $a572.80285 701 $aElloumi$b Mourad$0949311 701 $aZomaya$b Albert Y$0521938 801 0$bMiAaPQ 801 1$bMiAaPQ 801 2$bMiAaPQ 906 $aBOOK 912 $a9910139396103321 996 $aAlgorithms in computational molecular biology$92170898 997 $aUNINA