Genome databases

• References: NCBI databases, Ensembl database
• UCSC Genome Informatics: genome browsers and BLAT
• Entrez Genomes from NCBI: a portal to lots of genome data
• NCBI Human Genome information resources
• Ensembl Genome Browsers
• Nucleic Acid Research Database Issue, Database List, and Web Server Issue

Unix

• Introduction to Unix (University of Wisconsin-Milwaukee)
• Rule the World with 11 UNIX Commands
• Using the Unix Operating System 1 (Lincoln Stein)
• Using the Unix Operating System 2 (Rob Halgren)
• UNIXhelp for Users
• UNIX Tutorial for Beginners
• Pico (simple text editor) tutorial
• Complete Linux Commands List
• Unix Cheat sheet
• Demo commands from end of lecture 4

X windows (graphical Unix environment)

• Using X windows on hebrides/tak
• VNC: free X display system

Bioinformatics on hebrides/tak

• Connecting to hebrides/tak and transferring files (including sources of software to do this)
• BLAST documentation: details about running NCBI's blastall, formatdb, and fastacmd
• EMBOSS: The European Molecular Biology Open Software Suite
• Local biological tools: program list and help pages
• Local database list: choices for local BLAST
• rmHTMLtags.csh: shell script to remove HTML tags from BLAST reports