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Super Link: MBS --> Molecular Biology Shortcuts Tools Page.
Basically everything you need to manipulate sequences: on-site tools and selected links






Search NCBI Databases

nucleotide query Search for a nucleic acid sequence 
protein query Search for a protein sequence 

Sequence Retrieval System EMBL, not simple

Sequences of plasmids/vectors

Vector Database Sequences of vectors used in Molecular Biology

Mangone's plasmid Data-Bank Sequences, maps and info's for many commonly used plasmids

Invitrogen vectors Searchable batabase of Invitrogen vectors. Includes Sequences, maps, restriction data and additional informations.

Stratagene Vectors Maps and sequences of pBluescript and other Stratagene cloning vectors

An effective way of finding informations, maps and sequences related to an expression/cloning vector is simply to use a meta search engine. It works very well if you know the precise name of the vector. Have a try:

Search The Web:


Bank-It Submit a sequence to GenBank






The PredictProtein Server Columbia

Transmembrane segments prediction Stockholm University

SignalP Predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms

PSORT Prediction of protein localization sites in cells

PhosphoBase Predicts protein phosphorilation sites.CBSA, Denmark

NetOglyc Predicts protein O-glycosilation sites. CBSA

PREDATOR Secondary structure prediction

PFAM Sanger Center. Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains

Search for MOTIFS in your protein sequence

Search databases with a motif

The ProDom Protein Domain Database






Gapped Blast NCBI
--> Compare two sequences using Blast                                                                                    

Blast Search DDBJ. DNA Data Bank of Japan  
Blast Search EMBL 
Blast Search Expasy
Blast Search ISREC WU-BLAST server  
Blast Search Pasteur 
Blast Search Genestream@IGH, France

C. elegans Blast Server At the Sanger Centre: Search the DNA database containing C. elegans sequence data from both the Cambridge and St. Louis Sequencing groups. Also available are the current database of C. elegans ESTs and the C. elegans protein database (wormpep).


PSI-BLAST Position Specific Iterated BLAST. DDBJ







BCM pairwise alignment                                                                                           

Clustalw 1.7 : Multiple Alignements@Pasteur

Clustalw EBI

MBSaligner A nice interface to crustalw multiple sequence alignment software






ESTblast hgmp, make EST contigs, account required

IMAGE clone search and request EST clones 

IMAGE Vectors Sequences of the vectors used for the EST libraries 

protEST search EST databases with a protein sequence

STACK Identifies EST contigs from an imput sequence

The EST Assembly Machine TIGEM                                                                         

LabOnWeb Submit an EST/mRNA sequence to LabOnWeb. LabOnWeb elongates your sequence and provides you with a comprehensive report about your gene that includes a list of tissues in which the gene is probably expressed, guesses about gene function, mapping and more.






GenomeWeb HGMP, UK. Links to genome centers and resources for gene mapping

Uni-Gene Human Database

Genomic and Genetic Resources on the www At the National Human Genome Research Institute

Genome sequencing Center Washington University School of Medicine

MIT Center for Genome Research

GOLD: Genomes OnLine Database Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding complete and ongoing genome projects around the world. With information on 245 genomes, and over 2,000 web-links, GOLD provides the most detailed and accurate monitoring of genome sequencing projects.






Primer3 Input selection of PCR oligos, old version

Primer3 Tigem version

Oligo Calculator Calculate TM, %GC, picomoles/OD

Web Based Primerfinder V0.06 Primerfinder is a fast and easy web based primer design program. Primerfinder can search any sequence you input for primers that meet your specifications according to several search parameters. You can specify a target primer length, annealing temp, percent GC and many other advanced search parameters. Additionally, Primerfinder can analyze candidate primers with Integrated DNA Technology's Oligo Analyzer (powered by DNASTAR) for possible hairpin and self-dimer formation. Primerfinder can also examine primers you have already created by other means with IDT's Oligo Analyzer.                                                                   

Primers! Web interface

NetPrimer Comprehensive primer analysis, use it online or download






WEB Cutter performs restriction mapping of your DNA Sequence

TACG Restriction maps your DNA Sequence. A bit complex but quite exhaustive. Many different output formats. This is the primary TACG site. It is worthwhile to have a look at the documentation
TACG interface @Pasteur Bioweb

CloneIt! An online program finding sub-cloning strategies, in-frame deletions and frameshifts using restriction enzymes and DNA polymerases

ENZFINDER at MBS Searches REBASE database for known restriction enzymes matching your query. It provides informations on: isoschizomers and related enzymes, recognition sequences, methylation, commercial availability, references

Translation Machine EBI
Six frame translation tool
Reverse complement tool

ORF Finder Smart graphic output 
Grail form Detects valid open reading frames 
Genetic code Standard Genetic Code

Transcriptional Element Search Software Identifies transcription factors binding sites on your DNA sequence

Splice site prediction by Neural Network LBNL, US

Color Protein Sequence Based on hydrophobicity, charge, and other features of your choice

WWW Promoter Scan Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences.






A Guide to Molecular Sequence Analysis

Amos Bairock List of Links More databases exist than you ever imagined!

Computational services at EMBL 

exPASy DNA and Protein tools Top-Class site

Karolinska Institute Sequence Analysis Computer "KISAC is a bioinformatics facility, for computer aided analysis of nucleotide and protein sequences. It is used by about 40 research groups (150-200 researchers), mainly from the Karolinska Institute (KI) and the Karolinska Hospital (KS), although we have customers spread throughout Sweden"

LabOnWeb.com Beta version. A simple query procedure - just submit an EST/mRNA sequence to LabOnWeb - saves you months of time at the bench. The LabOnWeb research engine automates sequence elongation and delivers a wealth of information about the full gene derived from your input sequence.

Mac Software for Molecular biology

Molecular Biology Shortcuts


Network Protein Sequence Analysis NPSA. Many tools for similarity searches, secondary structure prediction and multiple sequence alignments.Pole Bio-Informatique lyonnais

Other Bio-Links

Protein Data Bank PDB. The single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.

Protein Information Resource PIR

Protein Research Foundation

List of servers useful for sequence analysis Genethon, France

TIGEM Many local tools and links to remote tools. Excellent resources for EST analysis

UK MRC Human Genome Mapping Project Resource Center Account required






Fly Base Heaven of D. melanogasterGenomics                                                               

Berkeley Drosophila Genome Project






Yeast Codon Usage

MIPS Yeast Genome Project

Saccaromyces Genome Database

Yeast Cloning Vectors

Search for yeast GenBank

S. cerevisiae Codon Usage

Yeast Genome Browser

Yeast Sequencing at the Sanger Centre

The Definitive Yeast Transformation Homepage

Yeast Lab Protocols from Gottschling Lab

Links to Saccharomyces cerevisiae Labs

Italian Yeast Cooperation Group

Yale Genome Analysis Center This web site is devoted to a project for large-scale analysis of gene expression, protein localization and disruption phenotypes in Saccharomyces cerevisiae


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