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!