Sequence Analysis in a Nutshell: A Guide to Tools and Databases

Overview

Gene sequence data is the most abundant type of data available, and if you're interested in analyzing it, you'll find a wealth of computational methods and tools to help you. In fact, finding the data is not the challenge at all; rather it is dealing with the plethora of flat file formats used to process the sequence entries and trying to remember what their specific field codes mean. If you survive by surrounding yourself with well-thumbed hard copies of readme files or remembering exactly where to look for the ...

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Overview

Gene sequence data is the most abundant type of data available, and if you're interested in analyzing it, you'll find a wealth of computational methods and tools to help you. In fact, finding the data is not the challenge at all; rather it is dealing with the plethora of flat file formats used to process the sequence entries and trying to remember what their specific field codes mean. If you survive by surrounding yourself with well-thumbed hard copies of readme files or remembering exactly where to look for the details when you need them, then Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases is for you. This book is a handy resource, as well as an invaluable reference, for anyone who needs to know about the practical aspects and mechanics of sequence analysis.

Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases pulls together all of the vital information about the most commonly used databases, analytical tools, and tables used in sequence analysis. The book is partitioned into three fundamental areas to help you maximize your use of the content. The first section, "Databases" contains examples of flatfiles from key databases (GenBank, EMBL, SWISS-PROT), the definitions of the codes or fields used in each database, and the sequence feature types/terms and qualifiers for the nucleotide and protein databases.

The second section, "Tools" provides the command line syntax for popular applications such as ReadSeq, MEME/MAST, BLAST, ClustalW, and the EMBOSS suite of analytical tools. The third section, "Appendixes" concentrates on information essential to understanding the individual components that make up a biological sequence. The tables in this section include nucleotide and protein codes, genetic codes, as well as other relevant information.

Written in O'Reilly's enormously popular, straightforward "Nutshell" format, this book draws together essential information for bioinformaticians in industry and academia, as well as for students. If sequence analysis is part of your daily life, you'll want this easy-to-use book on your desk.

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Product Details

  • ISBN-13: 9780596004941
  • Publisher: O'Reilly Media, Incorporated
  • Publication date: 1/28/2003
  • Series: In a Nutshell (O'Reilly) Series
  • Edition description: 1ST
  • Pages: 304
  • Product dimensions: 6.54 (w) x 9.14 (h) x 0.69 (d)

Meet the Author

Scott Markel is a Principal Software Architect at LION bioscience Inc., where he is responsible for providing architectural direction in the development of software for the life sciences, including the use and development of standards. He is a co-chair of the Life Sciences Research Domain Task Force of the Object Management Group, and also chairs the LSR's Architecture and Roadmap Working Group. Prior to working at LION, Scott worked at NetGenics, Johnson & Johnson Pharmaceutical Research & Development, and Sarnoff Corporation. He has a Ph.D. in mathematics from the University of Wisconsin-Madison. When Scott's not working or writing he enjoys spending time with his wife and kids, reading European history books, and just enjoying life in sunny San Diego.

Darryl León is a Principal Scientific Architect at LION bioscience Inc., where he is responsible for providing scientific direction in the development of software for the life sciences. Prior to working at LION, Darryl worked at NetGenics, DoubleTwist, and Genset. He has taught at California Polytechnic State University, San Luis Obispo, and currently teaches a bioinformatics class at U.C. Santa Cruz Extension and U.C. San Diego Extension. He is also a member of the Bioinformatics Advisory Committee at U.C. San Diego Extension. Darryl has a Ph. D. in biochemistry from the University of California, San Diego and did his postdoctoral research at the University of California, Santa Cruz.

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Table of Contents

Preface;
Sequence Analysis Tools and Databases;
How This Book Is Organized;
Assumptions This Book Makes;
Conventions Used in This Book;
How to Contact Us;
Acknowledgments;
Data Formats;
Chapter 1: FASTA Format;
1.1 NCBI’s Sequence Identifier Syntax;
1.2 NCBI’s Non-Redundant Database Syntax;
1.3 References;
Chapter 2: GenBank/EMBL/DDBJ;
2.1 Example Flat Files;
2.2 GenBank Example Flat File;
2.3 DDBJ Example Flat File;
2.4 GenBank/DDBJ Field Definitions;
2.5 EMBL Example Flat File;
2.6 EMBL Field Definitions;
2.7 DDBJ/EMBL/GenBank Feature Table;
2.8 References;
Chapter 3: SWISS-PROT;
3.1 SWISS-PROT Example Flat File;
3.2 SWISS-PROT Field Definitions;
3.3 SWISS-PROT Feature Table;
3.4 References;
Chapter 4: Pfam;
4.1 Pfam Example Flat File;
4.2 Pfam Field Definitions;
4.3 References;
Chapter 5: PROSITE;
5.1 PROSITE Example Flat File;
5.2 PROSITE Field Definitions;
5.3 References;
Tools;
Chapter 6: Readseq;
6.1 Supported Formats;
6.2 Command-Line Options;
6.3 References;
Chapter 7: BLAST;
7.1 formatdb;
7.2 blastall;
7.3 megablast;
7.4 blastpgp;
7.5 PSI-BLAST;
7.6 PHI-BLAST;
7.7 bl2seq;
7.8 References;
Chapter 8: BLAT;
8.1 Command-Line Options;
8.2 References;
Chapter 9: ClustalW;
9.1 Command-Line Options;
9.2 References;
Chapter 10: HMMER;
10.1 hmmalign;
10.2 hmmbuild;
10.3 hmmcalibrate;
10.4 hmmconvert;
10.5 hmmemit;
10.6 hmmfetch;
10.7 hmmindex;
10.8 hmmpfam;
10.9 hmmsearch;
10.10 References;
Chapter 11: MEME/MAST;
11.1 MEME;
11.2 MAST;
11.3 References;
Chapter 12: EMBOSS;
12.1 Common Themes;
12.2 List of All EMBOSS Programs;
12.3 Details of EMBOSS Programs;
12.4 aaindexextract;
12.5 abiview;
12.6 alignwrap;
12.7 antigenic;
12.8 backtranseq;
12.9 banana;
12.10 biosed;
12.11 btwisted;
12.12 cai;
12.13 chaos;
12.14 charge;
12.15 checktrans;
12.16 chips;
12.17 cirdna;
12.18 codcmp;
12.19 coderet;
12.20 compseq;
12.21 cons;
12.22 contacts;
12.23 cpgplot;
12.24 cpgreport;
12.25 cusp;
12.26 cutgextract;
12.27 cutseq;
12.28 dan;
12.29 dbiblast;
12.30 dbifasta;
12.31 dbiflat;
12.32 dbigcg;
12.33 degapseq;
12.34 descseq;
12.35 dichet;
12.36 diffseq;
12.37 digest;
12.38 distmat;
12.39 domainer;
12.40 dotmatcher;
12.41 dotpath;
12.42 dottup;
12.43 dreg;
12.44 einverted;
12.45 embossdata;
12.46 embossversion;
12.47 emma;
12.48 emowse;
12.49 entret;
12.50 eprimer3;
12.51 equicktandem;
12.52 est2genome;
12.53 etandem;
12.54 extractfeat;
12.55 extractseq;
12.56 findkm;
12.57 freak;
12.58 funky;
12.59 fuzznuc;
12.60 fuzzpro;
12.61 fuzztran;
12.62 garnier;
12.63 geecee;
12.64 getorf;
12.65 helixturnhelix;
12.66 hetparse;
12.67 hmmgen;
12.68 hmoment;
12.69 iep;
12.70 infoalign;
12.71 infoseq;
12.72 interface;
12.73 isochore;
12.74 lindna;
12.75 listor;
12.76 marscan;
12.77 maskfeat;
12.78 maskseq;
12.79 matcher;
12.80 megamerger;
12.81 merger;
12.82 msbar;
12.83 mwcontam;
12.84 mwfilter;
12.85 needle;
12.86 newcpgreport;
12.87 newcpgseek;
12.88 newseq;
12.89 noreturn;
12.90 notseq;
12.91 nrscope;
12.92 nthseq;
12.93 octanol;
12.94 oddcomp;
12.95 palindrome;
12.96 pasteseq;
12.97 patmatdb;
12.98 patmatmotifs;
12.99 pdbparse;
12.100 pdbtosp;
12.101 pepcoil;
12.102 pepinfo;
12.103 pepnet;
12.104 pepstats;
12.105 pepwheel;
12.106 pepwindow;
12.107 pepwindowall;
12.108 plotcon;
12.109 plotorf;
12.110 polydot;
12.111 preg;
12.112 prettyplot;
12.113 prettyseq;
12.114 primersearch;
12.115 printsextract;
12.116 profgen;
12.117 profit;
12.118 prophecy;
12.119 prophet;
12.120 prosextract;
12.121 pscan;
12.122 psiblast;
12.123 rebaseextract;
12.124 recoder;
12.125 redata;
12.126 remap;
12.127 restover;
12.128 restrict;
12.129 revseq;
12.130 scopalign;
12.131 scope;
12.132 scopnr;
12.133 scopparse;
12.134 scoprep;
12.135 scopreso;
12.136 scopseqs;
12.137 seealso;
12.138 seqalign;
12.139 seqmatchall;
12.140 seqnr;
12.141 seqret;
12.142 seqretsplit;
12.143 seqsearch;
12.144 seqsort;
12.145 seqwords;
12.146 showalign;
12.147 showdb;
12.148 showfeat;
12.149 showorf;
12.150 showseq;
12.151 shuffleseq;
12.152 sigcleave;
12.153 siggen;
12.154 sigscan;
12.155 silent;
12.156 skipseq;
12.157 splitter;
12.158 stretcher;
12.159 stssearch;
12.160 supermatcher;
12.161 swissparse;
12.162 syco;
12.163 textsearch;
12.164 tfextract;
12.165 tfm;
12.166 tfscan;
12.167 tmap;
12.168 tranalign;
12.169 transeq;
12.170 trimest;
12.171 trimseq;
12.172 union;
12.173 vectorstrip;
12.174 water;
12.175 whichdb;
12.176 wobble;
12.177 wordcount;
12.178 wordmatch;
12.179 wossname;
12.180 yank;
12.181 References;
Appendixes;
Nucleotide andAmino Acid Tables;
Nucleotide Codes;
Amino Acid Codes;
References;
Genetic Codes;
The Standard Code;
Vertebrate Mitochondrial Code;
Yeast Mitochondrial Code;
Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code;
Invertebrate Mitochondrial Code;
Ciliate, Dasycladacean, and Hexamita Nuclear Code;
Echinoderm and Flatworm Mitochondrial Code;
Euplotid Nuclear Code;
Bacterial and Plant Plastid Code;
Alternative Yeast Nuclear Code;
Ascidian Mitochondrial Code;
Alternative Flatworm Mitochondrial Code;
Blepharisma Nuclear Code;
Chlorophycean Mitochondrial Code;
Trematode Mitochondrial Code;
Scenedesmus Obliquus Mitochondrial Code;
Thraustochytrium Mitochondrial Code;
References;
Resources;
Web Sites;
Books;
Journal Articles;
Future Plans;
Colophon;

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