Part II: Tools

Now that we've described the common data formats and databases, it's time to get to work! What can you do with the data? You can compare two or more sequences, compute properties for the sequences, and look for patterns and subsequences. The possibilities are nearly limitless.

Since there's no way to describe all of the available tools or even just the ones we use we decided to showcase the tools we use most. We've included the classics: Readseq, BLAST, ClustalW, and HMMER. We also cover MEME and MAST (two tools that deserve to be better known), and a rising star called BLAT. The final chapter contains a wealth of information about the widely used open source suite of EMBOSS tools.

Each tool's brief description is followed by examples and command-line options. We've also included helpful web sites and other references.

We'd like to thank all the developers for making this rich abundance of documentation available to users!

Chapter 6

Chapter 7

Chapter 8

Chapter 9

Chapter 10

Chapter 11

Chapter 12



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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