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.
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Bio-Tools
PCR related
Sequence manipulation:
Restriction digest
Sequence alignments
Sequence similarity searches
Phylogenie related
Server on the net
Services at UAlberta.ca
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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.
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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.
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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.
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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.
INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY (IUPAC)
Good starting points for on-line analysis:
123genomics has an extended collection of links.
- 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
- includes:
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Protein Translator for
determining the protein sequence encoded by a DNA or RNA sequence.
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Restriction mapper for
determining the locations of restriction sites in a given DNA sequence.
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Sequence Pattern
Finder for locating sequences matching a particular pattern in a given DNA sequence. Includes REVERSE
TRANSLATION.
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Sequence
Massager for formatting and otherwise manipulating nucleic acid sequences.
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Secret Coder/Decoder
for translating top secret messages into DNA format and back.
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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.
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PCR Master Mix
Calculator for figuring out the amounts of each reagent to use in a two-dimensional box titration for
PCR.
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The BobCoTM
Database of sequences of control DNA molecules.
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ProtParam tool
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ProtScale
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Prosite
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TagIdent tool (formerly
GuessProt)
TagIdent is a tool which allows
- the generation of a list of proteins close to a given pI and Mw,
- 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,
- the identification of proteins by their mass, if this mass has been determined by mass
spectrometric techniques
From the biomolecule to the biosphere ... (closed since 13.06.2006)
alternative link
A gene network for navigating the literature. Get a description here.
Emboss
Disorder
Databases
Vector databases
Structure
Antibody databases
Are you working with membrane proteins(?):
Chemistry related stuff
Literature related
Information
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