Genome browser:
http://genome.ucsc.edu/index.html
RepeatMasker:
http://ftp.genome.washington.edu/cgi-bin/RepeatMasker
PipMaker:
http://nog.cse.psu.edu/pipmaker/
Vista:
http://pga.lbl.gov/vista.html
Regulatory Sequence Analysis:
http://rsat.scmbb.ulb.ac.be/rsat/
Marshfield Clinic:
http://research.marshfieldclinic.org/genetics/
Rockefeller Genetic Linkage Analysis Programs
http://linkage.rockefeller.edu/
Linux Tutorial
http://jgo.local.net/LinuxGuide/
Generic Model Organism Database Construction Set
http://www.gmod.org/
Linux Process Management & File Transfer (by Dmitriy Leyfer of Boston Uni) - part of Linux Bootcamp
http://zlab.bu.edu/~dmitriyl/bootcamp.htm
Introductory Perl Tutorial
http://w3.one.net/~bilshell/perlclass/syllabus.html
Beginning CGI Programming in Perl
http://www.cs.cf.ac.uk/Dave/PERL/node194.html
Advanced CGI
http://modperl.com:9000/perl_conference/advanced/handout.html
Stanford's SOURCE
http://genome-www5.stanford.edu/cgi-bin/SMD/source/sourceSearch
NCBI:
http://www.ncbi.nlm.nih.gov/
Gene Regulation (TRANSFAC, TRANSPATH, TRANSCompel)
http://www.gene-regulation.de/
Yahoo email:
http://mail.yahoo.com
Other bioinfo links (Prashanth Vishwanath of BU):
http://zlab.bu.edu/~vishy/toolpage.html
Bioinfo Software Downloads page (Suresh Kumar):
http://www.oocities.org/bioinformaticsweb/downloads.html
Jackson Laboratory:
http://www.informatics.jax.org/
Weizmann Institute of Science Bioinfo Links (GeneCard), Israel:
http://bioinfo.weizmann.ac.il/bioinfo.html
Molec Bio Databases:
http://bioinformatics.weizmann.ac.il/mb/tutorials.html
EMBL:
http://www.ebi.ac.uk/
Ensembl:
http://www.ensembl.org/
Genome Database: (retired - no new updates)
http://www.gdb.org/
IUBio @ Indian University:
ftp://iubio.bio.indiana.edu/
Search Launcher at Baylor College of Medicine:
http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher
home of SwissProt, ProSite and home to a collection of useful database analyses functions, especially for protein data:
http://expasy.hcuge.ch/
Emboss - The European Molecular Biology Open Software Suite:
http://www.uk.embnet.org/Software/EMBOSS/
RasMol/Protein Explorer:
http://www.umass.edu/microbio/rasmol/