Downloads
Links to useful sites
Links to useful protocols and tables
Links to useful programs
 
 
 

Downloads
Perl	Free download of Perl from ActiveSite
EngInSite	Free download of Perl Editor Lite from LuckaSoft
TextWrangler	Free download of a Text Editor for Mac OSX
Links to useful sites
Bioinformatics resources on web	Annotated list of web-based programs for analyzing DNA and protein sequences
Meme	Discovers motifs within sets of unaligned sequences
Molecular Toolkit	Colorado State's collection of useful tools to manipulate DNA and protein sequences
NCBI	National Center for Biotechnology Information: Home of Blast, Entrez, much else
Perl - Beginning Perl	Link to site dedicated to Beginning Perl, by Simon Cozens
Perl - Documentation	Core documentation for Perl. Lots of stuff.
Perl - Introduction	Short explanation of basic Perl features
BioPerl	Repository of Perl code that bioinformaticians have found useful
Directions for accessing Learning Perl	Excellent referenence manual freely available through library
Protocols and Tables
Download Adobe Acrobat	You probably already have Acrobat on your computer, but if you can't read PDF files, try downloading a free copy.
Genetic code	Useful on line reference to recall code, types of amino acids, and their abbreviations
How to download Perl	You can use Perl on a server, but you might be happier having a free copy on your own computer. There will be some exercises where you'll NEED your own copy.
How to write/run a program	Entering a program on your own computer and running it
How to download Blast	Get a copy of Blast for your own computer, to run genomic comparisons or other applications you can't do through the web version
How to download bacterial genomic databases	Access TIGR's set of completed bacterial genomes to download files containing complete list of proteins or complete DNA sequence
How to set up a database for Blast	Create a database consisting of set of proteins or DNA sequence. Use this database later as a target for Blast searches.
How to run Blast to compare genomes	Compare a set of proteins or DNA sequences to a local database.
Useful programs
Perl template	An outline into which you can plug a Perl program
ApE: A plasmid editor	A simple, but widely used sequence editor (never design sequences in Word!)
Serial Cloner	Another free sequence editor with slightly more functionality
4peaks	A very slick viewer and editor for sequence trace files (Electropherograms)
DR	(read DRectory) - useful in reading through massive files.
Papers for Mac	A very solid document management system for Mac...costs associated
Mendeley	Also a very good document manager, for Mac and PC and also FREE