Tools and Databases

International System of Units (SI-Units)

Standards, Units, Prefixes (NIST, USA)

Dehalococcoides strain CBDB1-Links

summarized Genome-Links (NCBI)
CBDB1 Annotation (MPI)
Pathways (KEGG)

Databases (Nucleic acids):

NCBI (database for eukaryotes and prokaryotes and many tools including ORF-Finder, electronic PCR, ..
NCBI-Entrez: Search across several databases
EBI (EMBL database and many tools. Also Links to other databases)
DDBJ - DNA Data Bank of Japan
CAMERA - Metagenome database of marine organisms

Databases (Proteins):

Expasy (Swiss-Prot database[Protein-sequences], many tools, many links)
UniProt (SwissProt, TrEMBL)
Protein data bank (PDB)

Databases (Metabolic pathways)

Boehringer metabolic pathways (Expasy)
Metabolic pathway maps (KEGG)

Taxonomy of bacteria

NCBI (16S rRNA-gene sequences)
GreenGenes

Alignments:

Alignment of sequences by ClustalW

Trees:

MEGA
arb
Treeview

Whole Genomes:

List of many sequenced prokaryotic genomes including further informations (TIGR) CMR
The Institute of Genomic Research (TIGR): Access to the genome of many different microbial genomes
Restriction analysis of whole genomes (TIGR)
Blast with prokaryotic genomes including unfinished genomes (TIGR-Blast)
NCBI Genomic blast (Taxonomy browser)
JGI Integrated Microbial Genomes

Genomes viewer/comparison:

Artemis
Artemis comparison tool (ACT)
WebACT
DoubleACT

Genome assembly:

Phed, Phrap: Sequence quality assignment and assemply
Consed: graphical assembly viewer

Blast:

Introduction
Blast NCBI-home

Tools:

Prediction of transmembrane helices
Prediction of signal sequences
further links useful for annotation
(HTM, 3,7 KB)
Annotation:

Interpro
Further Links (HTM, 3,7 KB)


DNA-libraries:

BACPAC Resources Center (BPRC): Resource for eukaryotic BAC and PAC libraries


Databases (Literature):

Pubmed [Literature-Database]
Web of Science [Literature-Database, only from TU-Computers]

Link collections by others:

#1 (NCBI-field guide)
#2 ICBM Oldenburg