Fungi

Links for consulting Fungi websites

•  SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast

• EUROSCARF collects yeast strains and plasmids that were generated during various yeast functional analysis projects

• Yeast Fitness Database - This site provides a graphical interface to the supplementary data presented in two publications:
  
  1. The Chemical Genomic Portrait of Yeast: Uncovering a phenotype for all genes
  2. Chemical genomic profiles predict gene function and mechanism of drug action

• Candida Genome Database -  a resource for genomic sequence data and gene and protein information for Candida albicans

Bacteria

Links for consulting Bacteria websites

• The Comprehensive Microbial Resource (CMR) is a free website used to display information on all of the publicly available, complete prokaryotic genomes

• MICrobial Advanced Database Organization (Micado) is a relational database dedicated to microbial genomes and functional analysis of Bacillus subtilis

• The Subtilist server is constructed around a database dedicated to the analysis of the genome of Bacillus subtilis.  Its purpose is to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments

• The Bacillus Genetic Stock Center (BGSC). Our primary mission is to maintain genetically characterized strains, cloning vectors, and bacteriophage for the genus Bacillus and related organisms

• Bacillus subtilis 168 Genome

• Pseudomonas aeruginosa is a versatile Gram-negative bacterium that grows in soil, coastal marine habitats, and on plant and animal tissues

• Pseudomonas putida KT2440 Genome

Nematodes

Links for consulting Nematode websites

• The Sanger Institute and the Genome Sequencing Center at the Washington University School of Medicine, St. Louis have collaborated to sequence the genomes of both C. elegans and C. briggsae
  
  
• Caenorhabditis elegans WWW Server
  

• The Caenorhabditis Genetics Center (CGC) is supported by the National Institutes of Health and National Center for Research Resources. The CGC has been in operation since 1978, first at the University of Missouri, Columbia and since 1992 at the University of Minnesota

• WormBase. Complete overview of Genes - Phenotype - Proteins - Genetics - Cells, Lineage, Pedigree - The Genome And Comparative Genomics- Sequences - Expression - Ontology - Reagents and Citations

• WormBook is a comprehensive, open-access collection of original, peer-reviewed chapters covering topics related to the biology of Caenorhabditis elegans and other nematodes

Vectors/Plasmids & Strains

Links for consulting Vectors/Plasmids & Strains websites

• The Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ). The microbial collections contain over 20, 000 cultures representing some 6,900 species and 1,400 genera (Archaea, Bacteria, plasmids, phages, yeasts, fungi)

• LGC Standards' partnership with ATCC facilitates the distribution of ATCC cultures and bioproducts to life science researchers throughout Europe

• The National BioResource Project E. coli Strain (NBRP) A collection of cloning vectors of Escherichia coli is kept at the National Institute of Genetics as a resource for the biological research community. Only those vectors that can be kept stably as DNA are collected. Therefore, we do not keep lambda phage vectors. Shuttle vectors are also not included because we don't have the facilities to verify their growth in organisms other than E. coli

• VectorDB contains annotations and sequence information for many vectors commonly used in molecular biology. Information for more than 2600 vectors is available with search facilities.

DNA - RNA - Protein

Links for consulting DNA - RNA & Protein analysis websites

• ExPASy Proteomics Server (Swiss Institute of Bioinformatics)

• External Scientific Toolkit (The Rockefeller University) provides a variety of bioinformatics applicationsand a web based scientific toolkit with links to numerous external bioinformatics resources

• Prosite Motif scanning means finding all known motifs that occur in a sequence. This form lets you paste a protein sequence, select the collections of motifs to scan for, and launch the search. A document deals with the interpretation of the match scores. You should consult the home pages of Prosite on ExPASy, Pfam and InterPro for additional information

• Gene Expression Atlas is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples

• Genevestigator is a user-friendly expression visualization tool answering two types of questions:
  
  1. Which conditions regulate my genes of interest
  2. Which genes are regulated by a chosen set of conditions

• Plasmapper - The PlasMapper server automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input

• PSORT is a computer program for the prediction of protein localization sites in cells. It receives the information of an amino acid sequence and its source orgin

• The Sequence Manipulation Suite (University of Alberta) is a collection of JavaScript programs for generating, formatting and analyzing short DNA and protein sequences

• Softberry - Softberry announces a pipeline for assembly and analysis of transcriptome data obtained using next generation sequencing technologies. The pipeline can be used to estimate gene expression levels, identify alternative splice variants, and improve gene proediction and genome annotation using transcription data

Bioinformatics

Links for consulting Bioinformatics websites

• BioGRID is an online interaction repository with data compiled through comprehensive curation efforts

• bioPIXIE is a general system for discovery of biological networks through integration of diverse genome-wide functional data

• T-profiler: Scoring the activity of pre-defined groups of genes using gene expression data. Gene expression data from Saccharomyces cerevisiae and Candida albicans are supported