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Web Tools for Molecular Biologists

Spot

Molbio

Lab protocols

(i) Lab SOPs

Real-time RT-PCR
ISH probe synthesis
Cloning of PCR products
Automated DNA sequencing
Southern blot hybridization
Northern blot hybridization
Primer extension
Competent cell preparation SOP
RNA extraction from medaka tissues

(ii) Commercial kits

3' and 5' RACE
Genome walking

(iii) Online protocols

Protocols by Kathryn Cheah's Lab
Molecular Biology Protocols
Protocol online

ISH & IHC

Dakocytomation
Alpha Diagnostic International, Inc.
Immunoportal.com
Genetech
Biochain
Nonradioactive In Situ Hybridization Application Manual - Roche
In situ hybridization protocol for various plant tissues - Guoping Shu

PCR technology

(i) Primer and probe design

Oligonucleotide Properties Calculator
OligoAnalyzer (IDT)
Primer3 - pick primers from a DNA sequence
CODEHOP - degenerate PCR primer design
Web Primer
mfold - predict secondary structure of beacons
Rules for designing degenerate PCR primers
RNAi design (IDT)
Database of validated primer sets for quantitative real-time PCR (Steve Johnson)

(ii) Real-time PCR

GENE QUANTIFICATION web page (Technische Universitat Munchen)
An excellent review article by SA Bustin (2000)
Technical notes by MT Dorak (2002)
The real-time TaqMan PCR and applications in veterinary medicine by CM Leutenegger
ABI PRISM 7700 tutorials
Roche LightCycler
BioRad iCycler
Ambion technical notes on real-time PCR
Qiagen SYBR Green detection systems
A technical article on fluorescence excitation and emission on IDT website

(iii) Basics

PCR Jump Station -abundant information and links on all aspects of PCR
BioGuide:PCR - Weizmann Institute of Science
Alkami PCR at Alkami Biosystems -free PCR resources for molecular biologists
DNA and PCR methods - NWFSC
PCR Applications Manual - Roche Applied Science
Technical tools for PCR - ABI
Amplification Assistant PCR Troubleshooting Program - Promega
PCR and Multiplex PCR: guides & troubleshooting - Octavian Henegariu, Yale

DNA/protein sequence analyses

(i) Most popular servers

NCBI
EMBL-EBI
BCM Search Launcher
ExPASy Molecular Biology Server

(ii) Sequence homology analaysis

BLAST (NCBI)
Align 2 sequences (NCBI)
Blast the medakafish genome (NBRP)
Blast the medaka genome (dolphin lab)
Blast the fugu genome (MRC HGMP RC)
Vega zebrafish genome blast (Sanger institute)
BLAST Search for TIGR Unique Gene Indices
EMBOSS pairwise global alignment (EBI)
Multiple sequence alignment by ClustalW (EBI)

(iii) Sequence utilities

Reverse complement
ReadSeq - converts to FASTA format (BCM)
Translate tool (ExPASy)

(iv) Restriction mapping

RestrictionMapper - restriction mapping
ReBase - information about restriction enzymes

(v) Protein utilities

Compute pI/Mw of a protein (ExPASy)
ProSite Scan (ExPASy) - domain search
EMatrix (Stanford)
Motif (Prosite, Blocks, Prodom, Prints, Pfam)  -  protein/DNA sequence motif search
NetPhos - phosphorylation site search

(vi) Search for transcription factor binding-sites

TFSEARCH (Japan)
TRES - comparative promoter analysis
TESS - Transcription Element Search System
Cluster Buster - dense clusters of motifs search
Signal Scan (NIH)
TraFaC
ConSite - search for transcription factor binding sites shared by two genomic sequences
PromoterWise (EMBL-EBI) - compares two DNA sequences allowing for inversions and translocations, ideal for promoters
PLACE - plant database
PredictRegulon - predict regulatory protein binding sites & operons in prokaryote genomes
Oligorep - oligonucleotids repeats finder

By Richard Yu

Research fellow

Centre for Marine Environmental Research and Innovative Technology (MERIT)
Department of Biology and Chemistry
City University of Hong Kong
Email: bhrichyu@cityu.edu.hk