Molecular Biology Web Sites
Top

General Molecular Biology Websites

Sites that link to other sites:

Online Tools @ molbiol-tools.ca
Has links to molecular biology pages all over the place.

More organised collections of Web resources:

BCM Search Launcher
The Baylor College of Medicine Search Launcher is an on-going project to organize molecular biology-related search and analysis services available on the WWW by function by providing a single point-of-entry for related searches.
SeWeR
SEquence analysis using WEb Resources. A unified interface for diverse web resources.
JustBio.com
Contains some hosted tools not present on the other mega-sites.

Bioinformatics Servers:

EBI Tools
Blast, Fasta, Sequence Analysis, Homology Searches, Sequence Translation, Protein Annotation, Genomes, Proteomes, Sequence Alignments, including Clustal.
Expasy
Proteomics server at Swiss Institute of Bioinformatics.
NCBI genomics Tools
NCBI's tools for genomics

Fly Stuff:

BDGP Analysis Tools page.
Search the Drosophila genome, predict genes etc.
Top

EMBOSS

The European Molecular Biology Open Software Suite:

EMBOSS homepage
Description of the EMBOSS suite.
 
EMBOSS Applications
...at the EMBNET node in Madrid.
 
EMBOSS Software via the WWW
...at University of Victoria.
Top

Primer Design
Primer 3 at Whitehead Institute
PCR primer selection tool.
dCAPS Finder 2.0
Web-based primer design for single nucleotide polymorphism analysis.
Top

Tandem Repeat Finders

Useful tool for finding potential STR polymorphisms:

Tandem Repeats Finder
" A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides. Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences."
 
Simple Sequence Repeats (SSR) Extractor Utility
The SSR Extractor utility finds simple sequence repeats within DNA sequences (loaded from any local Fasta file) and displays them in a table. The input data is processed according to several user-defined parameters. The output table is interactive and supports filtering, sorting, data re-processing and exporting to CSV format (Excel).
Top

DHPLC stuff
DHPLC tools @ Stanford
Useful things for designing amplicons for the WAVE machine
Transgenomic
Transgenomic's home page.
Top

Other stuff

Things to help with cloning and the like:

CloneIt!
A program for finding sub-cloning strategies, in-frame deletions and frameshifts using restriction enzymes and DNA polymerases.
Webcutter
Webcutter.
Top

Resources at Einstein

Servers:

Seqweb @ Harryeagle
seqweb on Harryeagle.aecom.yu.edu . No longer working - that's why I made this list.
Sequence Analysis @ AECOM
seqweb and GCG services at Einstein.

Lab web pages with useful links: Morrow | Greally |

Top

Bioinformatics Tutorials

How to use all this stuff:

2can
Bioinformatics Educational Resource at the European Bioinformatics Institute.
Online Lectures on Bioinformatics
The Max Planck Institute For Molecular Genetics provides an excellent course on bioinformatics.
BioActivity
Bioinformatics Web Practical at UMBER (University of Manchester Bioinformatics Education and Research).