Sequence similarity is a powerful tool for discovering biological function. Just as the ancient Greeks used comparative anatomy to understand the human body and linguists used the Rosetta stone to decipher Egyptian hieroglyphs, today we can use comparative sequence analysis to understand genomes. BLAST (Basic Local Alignment Search Tool), is a sophisticated software package for rapid searching of nucleotide and protein databases. It is one of the most important software packages used in sequence analysis and bioinformatics. Most users of BLAST, however, seldom move beyond the program's default parameters, and never take advantage of its full power.
BLAST is the only book completely devoted to this popular suite of tools. It offers biologists, computational biology students, and bioinformatics professionals a clear understanding of BLAST as well as the science it supports. This book shows you how to move beyond the default parameters, get specific answers using BLAST, and how to interpret your results. The book also contains tutorial and reference sections covering NCBI-BLAST and WU-BLAST, background material to help you understand the statistics behind BLAST, Perl scripts to help you prepare your data and analyze your results, and a wealth of tips and tricks for configuring BLAST to meet your own research needs. Some of the topics covered include:
Ian Korf received his B.A. from Cornell University and his Ph.D from Indiana University. His formal training is in molecular biology but he has had a fondness for computer programming since his early teens. His post-doctoral research at Washington University in St. Louis and at The Wellcome Trust Sanger Institute in the U.K. has focused on genomic sequence analysis with an emphasis on comparative genomics and gene prediction. His goal in life is to follow genomes, wherever they happen to take him.
Mark Yandell received his PhD in Molecular, Cellular and Developmental Biology from the University of Colorado, Boulder. After graduation, he joined the Genome Sequencing Center at Washington University, where he pursued post-doctoral studies in computational biology, genome annotation and SNP discovery. In 1999 he joined Celera Genomics, where he wrote much of the software used by Celera to annotate and analyze the drosophila, human, mouse and mosquito genomes. He recently joined the Berkeley Drosophila Genome Project.
Joseph Bedell received his B.S. in Genetics from the University of Georgia in 1991 then worked on mosquito genetics at the Centers for Disease Control and Prevention in Atlanta. He went on to complete a Ph.D. in human genetics at the University of California, Irvine in 1999. Joseph, like his co-authors, completed a post-doc in mammalian gene annotation with Warren Gish, one of the original developers of BLAST. He is currently the Director of Bioinformatics for Orion Genomics in St. Louis where he spends his days (and nights) using BLAST to answer important biological and phylogenetic questions in plants.
Our look is the result of reader comments, our own experimentation, and feedback from distribution channels. Distinctive covers complement our distinctive approach to technical topics, breathing personality and life into potentially dry subjects. The animal on the cover of BLAST is a coelacanth.The modern coelacanth, Latimeria chalumnae, is the sole living representative of Actinista, an ancient family of lobe-finned fish. The first live coelacanth was discovered off the east coast of South Africa in 1938 and caused a stir in the scientific community because they were believed to have been extinct for approximately 80 million years. A second, closely related species of coelacanths was found off the coast of Sulawesi in 1998.
Coelacanths grow to about 6 feet long; weigh up to 150 pounds; and are covered with bony, dark blue scales flecked with white. Coelacanths are unlike other living fish in that they have a three-lobed tail, fleshy fins, and a partially developed vertebral column. They are the only living vertebrate with a functional intercranial joint. It's this joint that allows the coelacanth's jaws to open exceptionally wide when inhaling its prey. Coelacanths are opportunistic predators (they eat whatever they can find) and are ovoviviparous (they give birth to live young).
From an evolutionary perspective, coelacanths are unique, and they provide a key perspective on the evolution of many different genes in vertebrate species. With their front and rear paired fins, which move in a similar fashion to the arms and legs of land vertebrates, coelacanths may be one of the closest links to those vertebrates that first crawled out of the sea to live on land more than 350 million years ago. Mary Anne Weeks Mayo was the production editor and proofreader, and Ann Schirmer was the copyeditor for BLAST. Derek DiMatteo, and Darren Kelly provided quality control. Lucie Haskins wrote the index.
Emma Colby designed the cover of this book, based on a series design by Edie Freedman. The cover image is an original illustration created by Lorrie LeJeune. Emma produced the cover layout with QuarkXPress 4.1 using Adobe's ITC Garamondfont.
David Futato designed the interior layout. This book was converted by Julie Hawks to FrameMaker 5.5.6 with a format conversion tool created by Erik Ray, Jason McIntosh, Neil Walls, and Mike Sierra that uses Perl and XML technologies. The text font is Linotype Birka; the heading font is Adobe Myriad Condensed; and the code font is LucasFont's TheSans Mono Condensed. The illustrations that appear in the book were produced by Robert Romano and Jessamyn Read using Macromedia FreeHand 9 and Adobe Photoshop 6. This colophon was compiled by Lorrie LeJeune.
This book's content is excellent and useful for biologist and computer guys who focus on sequences analysis. But there are some errors in the book, such as picture 3-5 in Charpter3. I also find a small bug in the example code of script "blast2table.pl". In the line 33, the q_align should assign to null value (q_align => ""),but the example code is a_align=>0 and perl treat "0" as a character
. So if you blast a 25bp oligo you will get an alignment length 26 wrongly. The code about q_align display in the Appednix E part is right.