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Bio-Tools
Useful links to servers on the net
that provide bioinformatics services
and links to free bioinformatics software.

Google search
of the CMBN web pages.

Bio-Tools

Sequence manipulation:

PCR related

qPCR related

Restriction digest Schere

Sequence alignments

Several online aligments can be done at the EMBL-EBI

Sequence similarity searches

Phylogenie related

Server on the net

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
  • MG-RAST
    MG-RAST (the Metagenomics RAST) server is an automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples.

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

NEB has some General Molecular Biology Data

The genetic code

INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY (IUPAC)

Good starting points for on-line analysis:

Bioinformatics Links Directory

ONLINE ANALYSIS TOOLS

SMART

String

123genomics has an extended collection of links.

Pedant

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

Terminator prediction

DNA/RNA fold prediction

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 BobCoTM Database of sequences of control DNA molecules.

ExPASy (Expert Protein Analysis System) Proteomics Server

  • ProtParam tool
  • ProtScale
  • Prosite 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

NIH

Institut Pasteur - Biological software

Information Hyperlinked over Proteins

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

Emboss

EMBOSS-GUI

EMBOSS explorer

  • As the halflife time of the web severs offering the EMBOSS explorer is relatively short you may want to do a do a Google search for "EMBOSS explorer" or have a look at the List of EMBOSS servers (based on EMBOSS Explorer)

fuzznuc - til Herman

Structure


Disorder

Function


  • ProFunc
    - prediction of protein function from 3D structure, at EMBL-EBI

Protocols im Topf rühren

Databases

Sequence databases

Vector databases

Structure

Strain databases

Antibody databases

Are you working with membrane proteins(?):

Chemistry related stuff

Literature related

Information


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Software
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