Over the past five years, these are some of the useful resources on the web that I have used. Here I make my compilation public hoping that it will be some use to others.
[Drosophila Stuff, Linux and Bioinformatics, Reference, Useful Tools, DNA Motif Search Tools]
Drosophila Stuff
- Links pertaining to Fruit fly research.
- Flybase
- The one stop shop for Drosophila resources.
- Fly Enhancer
- Useful tool for looking for specific transcription factor binding sites.
- FlyMove
- Watch movies and stuff about fly development.
- Flynet Server
- Check for Drosophila protein-protein interaction networks.
- Fly Target Explorer
- Wonderful resource in which one can program and generate Position Weight Matrices for TF motifs, and search the fly genome with it. Including comparisons with closely related Drosophila species.
- Drosophila Research Conference
- Annual Drosophila Research Conference Home Page.
- bionet.drosophila
- Google Group pertaining to Drosophila research.
- Drosophila.htm
- Bunch of fly links.
- P-Screen Database
- Good resource for finding P-Lines of mutants in required Drosophila genes.
- Fruit Fly Genetics
- Reference primer on fly pushing.
- The interactive Fly database
- Like the flybase, but more about the fly anatomy
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Big Facilities.
- NCBI
- The one stop shop.
- Microarray Core Facility, UMBI, CBR
- They help print and hybridize microarrays for a fee.
Linux and Bioinformatics
- Bioinformatics.Org
- Lots of Bioinformatics stuff here.
- VigyaanCD.org
- Pretty good knoppix distribution packaged with bioinformatics tools.
- The European Bioinformatics Institute EMBL
- A place to do searches and other bioinformatics stuff
- Center for Bioinformatics
- Has some statistical tools.
- comp.os.linux
- Google group on linux.
- LinuxCommand.org: Learning the shell.
- The Linux Cookbook
- Tips and Techniques for Everyday use.
- freshmeat.net
- A good place to look for the latest software from the open source team.
- DSL/Cable Webserver
- A good tutorial on setting up and running your own webserver.
- KNOPPIX Linux Live CD
- Knoppix is great for those who occassionally need to boot up in Linux, but don't need performance.
- Mandriva Linux
- My first Linux distro. Very easy to install and user friendly.
- Ubuntu - Linux for Human Beings
- Very stable Debian based Distro, available in 64-bit.
- Gentoo Linux
- I have currently got this on a dual-boot set up, running in 64-bit on my machine.
Bio Jobs Folder
- The Institute for Genomic Research
- Career Opportunities - The Institute for Genomic Research
- WHO e-Recruitment
- Human Genome Sciences
- PDF Online
- Good resource to convert your resume to pdf.
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DNA Motif Search Tools
- MEME
- Finds patterns among groups of sequences, and outputs them with statistical significance.
- Pattern Discovery from Biosequences.
- Waiting for this tool to come on line.
- The Gibbs Motif Sampler
- Uses Gibbs Motifs to look for patterns in DNA.
- TESS : Transcription Element Search System
- Helps search for Transcription Factor Binding Motifs.
- TFSEARCH
- Searching Transcription Factor Binding sites.
- TF binding site links
- Links to tools that help predict TF binding sites.
- NF-kappaB transcription factor binding DNA-site
- Moderately useful site for finding NF-kB Binding motifs.
- REDUCE
- Heard a lot of good things about this site, but never managed to properly use it. Supposed to help find transcription factor binding sites. Use Netscape.
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Reference Section
- Lots of good reference sites.
- Genetic Code Quick Reference
- A quick reference to identify the Amino Acid corresponding to a DNA sequence.
- Genetics Glossary AB
- Look up unknown words for Genetics terms
- The WWW Virtual Library: Cell Biology
- MOCB640 Bookmarks
- Arlene Stolzfus Bioinformatics Links. Very useful.
- Molecular Biology Methods
- A lot of useful Molecular Biology Protocols.
- Bioprotocols
- A place to find how to do stuff
- NWFSC Molecular Biology Techniques Forums :: ...
- Ask questions about Molecular Biology Protocols here.
- Invitrogen
- You can already buy most of your stuff from here. At rate at which they are going, they will take over the world.
Miscellaneous Databases
- Bioinformatics Software on the Web
- Biolinks.html
- Celera - Human Genome Publication Site
- Codon Usage Database
- dbSNP Home Page
- Protein Mutant Database
- Search by Cross Taxa
- Welcome to the BigBlue Web site
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Useful Tools
- Primer3
- Great on-line tool for designing primers. I designed 600 pairs of primers for my spotted array using this, and they all worked!
- Oligonucleotide Properties Calculator
- This tool can help in primer design, by telling you annealing temperatures and stuff about the oligos you design.
- Sequences Alignments and Comparisons
- Compendium of different sequence alignment resources.
- Tools for Multiple Alignments
- Good resource for multiple alignments.
- Official REBASE Homepage
- Find out about Restriction Enzymes here
- Pfam library of Protein motifs
- Find the motifs that make up a protein
- RNA folding form
- Give them an RNA sequence, and they output its calculated secondary structure.
- Interactive Statistical Calculation Pages
- Perform a variety of different statistical functions here.
- BioCarta - Charting Pathways of Life
- Resource for seeing signal transduction cascades.
- New Scientist.com - The World's No. 1 Science...
- My favourite subscription. Readable bits of science, without creating misconceptions.
- ScientificJournal.com
- USUHS/LRC Remote Services Director
- Awesome resource if you have the password to get in.
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