February 5, 2003
New Book Provides a Compact Guide to Common Tools and Databases Used in Sequence Analysis: O'Reilly Releases "Sequence Analysis in a Nutshell"
Sebastopol, CA--You can distinguish a vulture from a hawk by its
dihedral wing profile. The mockingbird is easily differentiated from
similarly sized birds by the flash of white on its wings and its swift,
aerodynamic swoop from tree to tree. In the field, quick identification
is made possible with the use of field marks: know the field marks and
you'll know your bird. Likewise, you can recognize the bioinformatician
involved in sequence analysis by the surrounding clutter of
well-thumbed hard copies of readme files that help him or her to make
sense of the plethora of flat file formats used to process sequence
entries and to remember what the specific field codes mean. With the
wealth of tools available, often the bioinformatician's greatest
challenge is keeping them straight. But this is soon to change. The
release of Sequence
Analysis in a Nutshell: A Guide to Common Tools
and Databases by Scott Markel and Darryl Leon (O'Reilly, US $29.95)
does away, once and for all, with the stacks of notes and printed
reference papers. This book brings together all of the vital
information about the most commonly used databases, analytical tools,
and tables used in sequence analysis into one handy reference guide.
Gene sequence data is the most abundant type of data available, and
there is a rich array of computational methods and tools that can help
analyze patterns within that data. "Sequence Analysis in a Nutshell"
pulls together the detailed terms, definitions, and command-line
options found in the key databases and tools used in sequence
analysis. The book is partitioned into three fundamental areas to help
bioinformaticians maximize their use of the content. The first section,
"Databases," contains examples of flat files from key databases
(GenBank, EMBL, DDBJ, Pfam, PROSITE, and 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 "In a
Nutshell" format, this book provides essential information for
bioinformaticians in industry and academia, as well as for students.
"Sequence Analysis in a Nutshell" is a handy resource and an invaluable
reference for anyone who needs to know about the practical aspects and
mechanics of sequence analysis.
Sequence Analysis in a Nutshell
Scott Markel and Darryl Leon
ISBN 0-596-00494-x, 284 pages, $29.95 (US), $46.95 (CAN), 20.95 (UK)
O'Reilly Media spreads the knowledge of innovators through its books, online services, magazines, and conferences. Since 1978, O'Reilly Media has been a chronicler and catalyst of cutting-edge development, homing in on the technology trends that really matter and spurring their adoption by amplifying "faint signals" from the alpha geeks who are creating the future. An active participant in the technology community, the company has a long history of advocacy, meme-making, and evangelism.
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