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O'Reilly Media | BLAST
BLAST
Featured customer reviews
blast2table example error, January 25 2008
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 => "carview.php?tsp="),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.
Buy this Book
By Ian Korf, Mark Yandell, Joseph Bedell
First Edition
July 2003
Pages: 360
ISBN 10: 0-596-00299-8 |
ISBN 13: 9780596002992
(Average of 1 Customer Reviews)
BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs that explore all of the available sequence databases for protein or DNA. BLAST is the only book completely devoted to this popular and important technology and offers biologists, computational biology students, and bioinformatics professionals a clear understanding of this program. This book shows you how to get specific answers with BLAST and how to use the software to interpret results. If you have an interest in sequence analysis this is a book you should own.
Full Description
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:
Browse within this book
- 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
- Industrial-strength BLAST, including developing applications with Perl and BLAST
Cover | Table of Contents | Colophon
Featured customer reviews
blast2table example error, January 25 2008
Rating:
Submitted by
haiyan
[Respond | View]
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 => "carview.php?tsp="),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.
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