This page contains information and links to tools commonly used in the
field of bioinformatics.
These tools are hosted locally on our website.
BLAST server - Perform BLAST searches
against microbial genomes. Each of our public genome projects is
available, along with many of the well-studied microbial genomes.
Manatee - A
SourceForge app originally developed by TIGR, this is a web-based
program designed to assist in the annotation of both prokaryotic and
eukaryotic genomes. (Access to our setup is limited. You can download
manatee here)
Poisson calculator - A Perl script based
on the Poisson Distribution. Generally used to compute fold coverage
for genome projects.
SeqSeek v0.2 -
Positionally map a query sequence against a genome, relative to the genome's coding
regions, and view the results graphically or in an artemis applet.
Sequal v2.0 - Graph
and color-code the Phrap quality scores of a contig from unfinished
genome projects to find the best location for designing PCR experiments.
Setting up BLAST locally on
Mac OS X - Everything you need to know to be able to BLAST locally on your
computer, rather than over the web. Written for those who are absolute beginners
with unix-based operating systems.
Pipeline - An outline
briefly explaining how sequencing reads are processed at the Laboratory for Genomics
and Bioinformatics.
Artemis Review - Review of Artemis
4 written by Matt Carson for BioMedNet's HMS Beagle.
These are tools that people in bioinformatics or interested in it should probably be familiar
with. At the very least, we find them helpful and some are essential to
the operation of our core. (more to be added later)
ActivePerl - This is
ActiveState's easily installable distribution of PERL for Linux, Solaris, and
Windows. It contains the PERL language, Package Manager, and complete online
help. ActivePerl is free for all but ActiveState also offers a plug-in to Visual
Studio.NET called VisualPerl for a fee.
Artemis - Artemis, developed
by the Sanger Center, is a free annotation and DNA sequence visualization tool. It
is an invaluable tool for genome annotation. Because it is written in JAVA, and thus
highly portable, it is available for nearly all major operating systems. See Matt's
published Artemis review here.
Clustalw - A multi-alignment tool
for DNA or proteins.
Consed/autofinish - Available only for
UNIX, Consed is a graphical editor and autofinish an automated finishing
program for Phrap sequence assemblies (see Phred/Phrap below). Free only
for academic/non-profit use.
Phred/Phrap - A base-caller and assembler
used to assemble multiple sequences files into contigs for genomic sequencing.
Free only for academic/non-profit use.
TreeView
- Phylogenetic tree drawing software, available for 16 & 32-bit Windows,
Apple, and now Linux/UNIX.
The following are books we have found most helpful in autodidactic
training for bioinformatics. I'm sure there are others out there
that should be added to the list, but the authors have not yet
sent us our free copies for review. (come on! our address is clearly
printed here) When they do, we'll be sure
to add them to our list.
Beginning Perl for Bioinformatics (Tisdall, James D.) - Finally, a
book aimed towards biologists in Perl, arguably the bioinformatics language of
choice. An excellent book for those completely new to PERL, or programming
in general, and the examples given make it an excellent read for seasoned
programmers as well. (O'Reilly - ISBN 0596000804)
Bioinformatics: Sequence and Genome Analysis (Mount, David W.) - This is the best
one we've found yet; a must have for students interested in bioinformatics
and professionals doing it. It is used in many universities (including
ours) as a textbook in bioinformatics courses. Assumes an undergrad
background in biology and only fundamental experience in computing.
(Cold Spring Harbor Lab - ISBN 0879696087)
Bioinformatics: The Machine Learning Approach (Baldi, P., et al.) - Goes into detail
about many of the algorithms that make up bioinformatics; definitely
not for those who dozed during their advanced math courses. Good enough
though to already be in its second edition. (MIT Press - ISBN 026202506X)
Developing Bioinformatics Computer Skills (Gibas, Cynthia & Per Jambeck)
- A bit broad but still not a bad book for someone to explore their
interest in bioinformatics. Touches on most current issues and is a
good primer. (O'Reilly - ISBN 1565926641)
JAVA Programming: From the Beginning (King, K. N.) - A really good book to teach yourself
JAVA that doesn't assume you've already been programming in another
language for years. It serves as a textbook and has questions and exercises
at the end of the chapters. (WW Norton & Company - ISBN 0393974375)
Oracle 101 Series (various authors) - For those interested in databasing, this
series of books is the best out there for learning Oracle. They were
written to be learning books rather than clunky reference manuals and
cover everything from introductory database architecture to web-based
form programming. (Oracle Press - here)
Post-Genome Informatics (Kanehisa, Minoru) - (Oxford U. Press - ISBN 0198503261)
Statistical Methods In Bioinformatics: An Introduction (Grant, Gregory R., et
al.) - A good book for statistics, but probably leans a little in favor
of those with backgrounds in statistics rather than biology. A course
in statistics first would probably be needed to get some of the stuff
in here. (Springer Verlag - ISBN 0387952292)
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Microgen offers Bioinformatics Support through our Informatics Core. The rate for support is $75/hour with a one hour minimum charge. Please note
that we do not provide Tier 1 IT support.
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