Bio-Tools

• Centrifuge Helper 
• GraphPad Radioactivity Calculator 

PCR related

• OligoCalculator 
• Oligonucleotide Properties Calculator  , Home with latest version.
• Primer3 - Primer3Plus (Webinterfaces) - NCBI/ Primer-BLAST - more links
• Tm calculator for PCR Java must be activated in your browser!.
  recommended when setting up amplifications with Finnzymes' DyNAzyme, Phire and Phusion DNA Polymerases and DyNAmo qPCR Kits
• dnaMATE T_m prediction
• PRIDE Primer Design (PRIDE 1.2)
• Primo Multiplex - Multiplex PCR Primer Design
• IDT Scitools - Oligo Design and Analysis Tools
• IDT OligoAnalyzer
• OligoPerfect Designer from Invitrogen, for qPCR primer design
• AutoDimer Primer-dimer analysis
  You can also download the program and run it localy or use Oligo Explorer .

Sequence manipulation:

• Extended Nucleic Acid Sequence Massager 
• Sequence Pattern Finder
• fmtseq: A BioSeq File Format Converter
• Readseq (Java): Webservice at IUbio, EBI, NIH, BCM.

Restriction digest

• Webcutter (Sweden) (Italy) (Firstmarket)
• WatCut
• More cutter sites
• 
  Double Digest Finder List of NEB Restriction Enzymes
• 
  DoubleDigest™ - List of Fermentas Restriction Enzymes Reaction conditions (buffers)
• 
  Compatible Buffers (double digest) - Restriction/Modifying Enzymes and RNase Inhibitors
• 
  Restriction Enzymes
• Collection of Restriction Enzyme Buffer Systems

Sequence alignments

• Muscle
  
  • MUSCLE Web server
  • MUSCLE server at
• T-Coffee
  • BioASP
  • IGS-CNRS
  • EMBL - CH
  • T-Coffee server at
• Clustal
  • BioASP
  • EBI
  • GeneBee
  • BCM Search Launcher: Multiple Sequence Alignments
  • Pasteur
  • EMBL - CH
  • ClustalW server at
• GraphAlign

Sequence similarity searches

• ParAlign
• BLAST
  • BLAST with microbial genomes
  • BLAST two sequences

Phylogenie related

• PHYLIP
• Phylogeny Programs Lists at the Felsenstein lab, Department of Genome Sciences, University of Washington , Seattle
  • cross-referenced by method and by computer system.
• Links to Recombinant sequence Analysis/detection Programs
• 
  Interactive Tree Of Life

Server on the net

• Bioinformatics Toolkit
• Bioinformatics Toolkit
• Services in computational biology at the Nano+Bio Centre at the Universität in Kaiserslautern
• A collection of server for PROTEIN SECONDARY STRUCTURE
• BacMap: An Interactive Atlas for Exploring Bacterial Genomes

  BacMap is an interactive atlas of bacterial genomes. CGView is used to pre-render navigable maps of all sequenced bacterial genomes.

• PlasMapper

  The PlasMapper server automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input. Plasmid sequences up to 20,000 bp may be annotated and displayed. Plasmid figures may be rendered in PNG, JPG, SVG or SVGZ format. PlasMapper supports an extensive array of display options.

• CGView Server

  The CGView Server is a comparative genomics tool for circular genomes (plasmid, bacterial, mitochondrial, and chloroplast) that allows sequence feature information to be visualized in the context of sequence analysis results.

• 
  BioPortal at UiO
  • The applications currently installed

Annotation Systems

• BASys: Bacterial Annotation System

  BASys (Bacterial Annotation System) is a web server that performs automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences.

• SABIA - System for Automated Bacterial Integrated Annotation
• GenDB is a genome annotation system for prokaryotic genomes
• IGS Annotation Engine
• JCVI Annotation Service
• KAAS - KEGG Automatic Annotation Server

Antigenicity

• Predicting Antigenic Peptides

  This program predicts those segments from within a protein sequence that are likely to be antigenic by eliciting an antibody response. Antigenic peptides are determined using the method of Kolaskar and Tongaonkar (1990). Predictions are based on a table that reflects the occurrence of amino acid residues in experimentally known segmental epitopes. Segments are only reported if the have a minimum size of 8 residues. The reported accuracy of method is about 75%.
  OBS: The input sequence must be in CAPITAL LETTERS! Use the Sequence Massager to prepare you sequence.

• EMBOSS antigenic Finds antigenic sites in proteins.

EMBIO services

Some Calculations at molbiol.ru

has some General Molecular Biology Data

The genetic code

INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY (IUPAC)

• IUBMB Biochemical Nomenclature Database
• IUPAC Chemical Nomenclature and Recommendations on Organic & Biochemical Nomenclature, Symbols & Terminology
• IUPAC Nomenclature of Organic Chemistry

Good starting points for on-line analysis:

Bioinformatics Links Directory

ONLINE ANALYSIS TOOLS

SMART

String

123genomics has an extended collection of links.

Pedant

• Neisseria gonorrhoeae FA 1090
• Neisseria gonorrhoeae NCCP11945
• Neisseria meningitidis MC58
• Neisseria meningitidis Z2491
• Neisseria meningitidis 053442

MicrobesOnline

• MicrobesOnline includes gene expression data from microarrays: you can view up-regulated or down-regulated genes or operons, and you can view changes in expression patterns in a metabolic map.

Prokaryotic promoter prediction

• BPROM - Prediction of bacterial promoters
  
• Neural Network Promoter Prediction at www.fruitfly.org
  
• Prokaryotic promoter analysis using SAK
• PPP - perform promoter prediction on FASTA formatted DNA sequences
  
• List at molbiol-tools.ca

Terminator prediction

• TransTermHP

Sequence Analysis Software from Attotron Biosensor Corporation

• includes:
• Protein Translator for determining the protein sequence encoded by a DNA or RNA sequence.
• Restriction mapper for determining the locations of restriction sites in a given DNA sequence.
• Sequence Pattern Finder for locating sequences matching a particular pattern in a given DNA sequence. Includes REVERSE TRANSLATION.
• Sequence Massager for formatting and otherwise manipulating nucleic acid sequences.
• Secret Coder/Decoder for translating top secret messages into DNA format and back.
• Randomizing Homologous Recombiner for recombining any two input sequences. User enters a window size, and a probability value for recombination if the two sequences match within the sliding window.
• PCR Master Mix Calculator for figuring out the amounts of each reagent to use in a two-dimensional box titration for PCR.
• The BobCo^TM Database of sequences of control DNA molecules.

ExPASy (Expert Protein Analysis System) Proteomics Server

• ProtParam tool
• ProtScale
• Prosite
• TagIdent tool (formerly GuessProt)
  TagIdent is a tool which allows
  1. the generation of a list of proteins close to a given pI and Mw,
  2. the identification of proteins by matching a short sequence tag of up to 6 amino acids against proteins in the UniProt Knowledgebase (Swiss-Prot and TrEMBL) databases close to a given pI and Mw,
  3. the identification of proteins by their mass, if this mass has been determined by mass spectrometric techniques

BCM Search Launcher

Deambulum

From the biomolecule to the biosphere ... (closed since 13.06.2006)
alternative link

NIH

• NCBI Blast
• READSEQ Sequence Conversion

Institut Pasteur - Biological software

Information Hyperlinked over Proteins

A gene network for navigating the literature. Get a description here.

Emboss

EMBOSS-GUI

• Do a Google search for "EMBOSS-GUI".
• Uni Kiel
• GBF, (EMBOSS - NGFN-BLAST- main page)
• Linux-Daemon.de
• Uni Konstanz

EMBOSS explorer

• EMBOSS explorer at EMBnet Norway
• at bioinformatics.nl
• at UMDNJ
• at the Viral Bioinformatics Resource Center
• Do a Google search for "EMBOSS explorer" or have a look at the List of EMBOSS servers (based on EMBOSS Explorer)

fuzznuc - til Herman

• at Pasteur
• at AnaBench in Canada
• at es.EMBNET
• at HPA-Bioinfotools
• Google search for fuzznuc or have a look at the List of EMBOSS servers

Structure

• 
  The PredictProtein server (old version, old version)
• PSIPRED Protein Structure Prediction Server
• SWISS-MODEL
• WhatIf
• The ConSurf Server
• Jpred
• 
  Network Protein Sequence @nalysis
• CBS Prediction Servers
• phyre
• HMM-based Protein Structure Prediction, SAM-T08
• Biotech Validation Suite for Protein Structures

Disorder

• 
  Database of Protein Disorder
• Protein Disorder Predictors

Protocols

• OpenWetWare
  search
• Protocol online
• BioChemika Ultra (former MicroSelect)
  
  
  

  Introduction Amino Acids Antioxidants Biological Buffers	Carbohydrates Chelators Crystallization Denaturation	Detergents/Surfactan Density Gradient Molecular Biology	Luminescence Spectroscopy Reagents
  Useful pH Ranges of Selected Biological Buffers (25 °C, 0.1M) Trizma Buffer Table - pH vs. Temperature Phosphate Buffer Table - 0.2M solution Helpful Formulas

• pET System Manuals
• 
  Promega Protocols and Applications Guide
  The separate chapters are also downloadable as PDF files.
  Get a copy of the rev. 9/06 version, all chapters in one file, as a PDF file here (9,7 MB).
  Download revision 12/09 in A4 from here, letter here.

Databases

• EcoliWiki

Sequence databases

• 
  UniProt (Universal Protein Resource)
• Swiss-Prot
• 
  The Comprehensive Enzyme Information System
• repairGenes
• Genetic Code Viewer
• DNA Methylation Database
• G P M S - Genomes, Polymorphism and Minisatellites
• 
  SUPERFAMILY offers sequence searching, alignments and genome assignments.
• REBASE^® - The Restriction Enzyme Database
• Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families.
• Gene Ontology Browser
  • AmiGO
  • GO Browser
  • Search with Google for more Gene Ontology Browser
• 
  Encyclopedia of Escherichia coli K-12 Genes and Metabolism
• Ensembl produces and maintains automatic annotation on selected eukaryotic genomes.
• Magpie Automated Genomics Project Investigation Environment
• MLST, Neisseria MLST
• Meningococcal Typing
, PorA, PorB

Vector databases

• Addgene
• VectorDB
• Plasmid HomePage
• 
  Lineage (full): root; other sequences; artificial sequences;vectors

Structure

• 
  MMDB (Molecular Modeling DataBase) - Entrez's Structure Database - NCBI Structure
• Worldwide Protein Data Bank (wwPDB)
  • Protein Data Bank (PDB)
  • PDBSum
  • Proteopedia
• 
  THE MACROMOLECULAR STRUCTURE DATABASE - EMBL-EBI
• 
  Enzyme Structures Database - EBI

Strain databases

• StrainInfo

Antibody databases

• The Antibody Resource Page
• Acris-Antibodies
• Abcam
• Antibodies-Online, DE
• MyBiosource
• Linscott's Directory of Immunological & Biological Reagents

Are you working with membrane proteins(?):

• 
  TCDB: Transport Classification Database
• TMBETA-NET
• 
  Membrane Protein Resources
  • Membrane Proteins of known 3D structure
• BIOTOOLS
  • AveHas - Protein Average Hydropathy, Amphipathicity and Similarity Analysis
  • What - Protein Sequence Secondary Structure, Hydropathy and Amphipathicity Analysis
  • Memsat - Protein Transmembrane Helix Prediction
  • TMS_Align - Display TMS Distribution in Multiple Sequence Alignment

Chemistry related stuff

• PubChem Server Side Structure Editor
• ACD/Labs' freely available structure-drawing program ChemSketch

Literature related

• Web of Science
  Cited Reference Search
• Look up "Impact Factors"

Information

• About Nucleotide And Protein Sequence Formats (EBI)
• Sequence formats for EMBOSS

Jump to

• Alignments
• Sequence similarity searches
• Phylogenie
• Server on the net
• on-line analysis
• EMBOSS
• Structure
• Protocols
• Databases
• Membrane proteins
• Info

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• Free Software