- Taschenbuch: 368 Seiten
- Verlag: O'Reilly & Associates; Auflage: 1 (8. August 2003)
- Sprache: Englisch
- ISBN-10: 0596002998
- ISBN-13: 978-0596002992
- Größe und/oder Gewicht: 17,8 x 2,1 x 23,3 cm
- Durchschnittliche Kundenbewertung: Schreiben Sie die erste Bewertung
- Amazon Bestseller-Rang: Nr. 668.785 in Fremdsprachige Bücher (Siehe Top 100 in Fremdsprachige Bücher)
- Komplettes Inhaltsverzeichnis ansehen
BLAST (Classique Us) (Englisch) Taschenbuch – 8. August 2003
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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, 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" 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: BLAST basics and the NCBI web interface; how to select appropriate search parameters; BLAST programs: BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX, PHI-BLAST, and PSI BLAST; detailed BLAST references, including NCBI-BLAST and WU-BLAST; understanding biological sequences; sequence similarity, homology, scoring matrices, scores, and evolution; sequence alignment; calculating BLAST statistics; and industrial-strength BLAST, including developing applications with Perl and BLAST.
Über den Autor und weitere Mitwirkende
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.
Die hilfreichsten Kundenrezensionen auf Amazon.com
The book discusses the biology, statistics, algorithms, and computer science issues involved in explaining blast. I liked this approach because it does not head super far into any one core area but rather sticks to a strong fundamental overview of each topic. The other strong aspect of this book is that the author thoroughly compares NCBI and WU Blast throughout, characterizing instances where one may choose one over the other and/or how to tweak the parameters for both in those situations.
I orginally bought the book b/c I wanted an overview on PAM and BLOSUM matrices and to understand how Blast Statistics work. It really served as an informative contextual tutorial that has definitely raised my overall understanding on not only Blast, but to better grasp the very interdisciplinary nature concerning sequence alignment for in-silico biological research.
Good job! thanks amazon!
The book is poorly written and organized. The language is vague. Explanations are too short and incomprehensible for a new user. In explaining new concepts authors often use some unknown professional terms and notions, which they never explain. I could guess some terms after reading several times, but too much you have to guess. Some letters in formulas are not explained. Authors should have thought more about their readers.
Maybe this is a book for those who already know the subject, but it claims to be a comprehensive introduction. Also the authors claim that it is a book not for mathematicians. Having a background in statistics I have big problems understanding the material. Maybe that's exactly what they mean by "not for mathematician" - saying some words without adequate definitions?
But the theory part is not well organized. You may want to seek other book if you are interested in this part.