Databases

MPIC

Mitochondrial Protien Import Components (MPIC)

In the 2 billion years since the endosymbiotic event that gave rise to mitochondria, variations to the mitochondrial protein import machinery has occurred across different phyla. With an increasing number of species being sequenced, it is now possible to gain insight into the mitochondrial protein import components in way that was not possible before. The Mitochondrial Protein Import Component (MPIC) Database provides interactive information on the protein import apparatus of plant mitochondria from a variety of plant and non-plant species. Researchers can easily access and search MPIC to reveal orthologs to 75 components with transcriptomic, proteomic and evolutionary data across 24 species in one database. Thus, MPIC provides a simple and centralised resource for all components of the mitochondrial protein import apparatus to provide insight into each gene/protein function(s) throughout evolution.

suba

SubCellular Proteomic Database (SUBA)

The SubCellular Proteomic Database (SUBA) houses large scale proteomic and GFP localisation sets from cellular compartments of Arabidopsis. It also contains precompiled bioinformatic predictions for protein subcellular localisations. The current version is SUBA2

Rice DB - Oryza Information Portal

Rice DB: Oryza Information Portal presents a unified searchable database, linking gene loci to comprehensive annotations, transcript expression data, upstream promoter motifs, protein properties, sub-cellular localization and function. Links to phenotype information can also be found for confirmed organellar proteins in rice. Additionally, Rice DB also facilitates and integrates direct comparison of rice to Arabidopsis, based on orthology, allowing parallel comparison between these two model species within one database.

anno-j

ANNO-J

Anno-J is a genome annotation visualization application built using Web 2.0 technology (REST, AJAX and DHTML). It has been designed specifically with next-gen sequencing data in mind and can easily handle large amounts of short-read information. It is designed to run without installation in any modern W3C compliant browser, (Firefox, Safari, Mozilla, Camino or Opera), and allows flexible configuration of multiple tracks from data providers located anywhere on the internet. The program is currently in advanced Alpha-stage development and is expected to go Beta in early March 2008.

Arabidopsis Mitochondrial Protein Database (AMPDB)

Uilizing data from the plant scientific community and from our own experimental work, this database allows relational searching through a web interface of mitochondrial proteomic data from Arabidopsis.

The database also includes predictions of mitochondrial localistation, orthology mapping to other mitochondrial proteome sets from yeast, humans and the mitoichondrial progenitoir, Rickettsia.

AtGST

Arabidopsis GST Protein Family (AtGST)

This dataset outlines the 53 members of the Glutathione S-transferase (GST) family in Arabidopsis. The list is divided into their pre-defined subfamilies and also shows their levels of duplication throughout the genome.

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Research Tools

mascot

MASCOT

Mascot is a powerful search engine which uses mass spectrometry data to identify proteins from primary sequence databases.

phenyx

Phenyx

Phenyx is a software platform for the identification and characterization of proteins and peptides from mass spectrometry data specifically designed to meet the concurrent demands of high-throughput MS data analysis and dynamic results assessment.

blast

blast

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

emboss

emboss

EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.

sms2

sms2

The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing.

sewer

sewer

SeWeR is an acronym, stands for SEquence analysis using WEb Resources. For a refined mind, SeWeR is an integrated portal to common web-based services in bioinformatics.

improbizer

Improbizer

Improbizer searches for motifs in DNA or RNA sequences that occur with improbable frequency (to be just chance) using a variation of the expectation maximization (EM) algorithm.

metabolome-express

metabolome-express

MetabolomeExpress houses both private and public uncurated repositories as well as a curated database of peer-reviewed, published GC/MS metabolomics datasets. You may anonymously query the curated database of metabolite response statistics to find experiments of interest using tools in the Database Explorer. Experimental datasets may be examined in detail using the in-built Experiment Explorer which includes integrated tools for raw data visualisation, GC/MS library matching and statistical analysis.

ELN

ELN: OpenLab Electronic Notebook

ELN is our electronic lab book. In addition to simply taking notes you can also do calculations within ELN, drag in images, documents, spread sheets, etc. It allows you to link experiments and associate original data files with experiments. ELN also houses our lab protocols. It is searchable and can be accessed via the internet, which makes it easy to collaborate nationally and internationally and also allows former PEB researchers finish off projects.

If you are interested in using ELN, have suggestions for improvement or any other questions, please contact Ricarda ph: 6488 4457 / @: ricarda.fenske@uwa.edu.au

ECM

ECM data store

ECM is a data store for large and historic data sets. It allows you to manage and access your data via the internet and share them with other users, which simplifies collaborations and gives former PEB researchers to opportunity to finish off projects. Data hosted by ECM can be linked to experiments created in ELN.

If you are interested in using ECM, have suggestions for improvement or any other questions, please contact Ricarda ph: 6488 4457 / @: ricarda.fenske@uwa.edu.au

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Downloads

FileDescriptionAvailableSize
PEB-2012.AnnualReport-LoRes.pdf2012 Annual Report15/02/201317MB
PEB-2011_AnnualReport-LoRes.pdf2011 Annual Report15/02/20138MB