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- Associate Professor Wei Shi
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- A new regulator of stemness to create dendritic cell factories for immunotherapy
- Advanced methods for genomic rearrangement detection
- Control of cytokine signaling by SOCS1
- Defining the protein modifications associated with respiratory disease
- Delineating the pathways driving cancer development and therapy resistance
- Developing a new drug that targets plasmacytoid dendritic cells for the treatment of lupus
- Development and mechanism of action of novel antimalarials
- Development of a novel particle-based malaria vaccine
- Development of tau-specific therapeutic and diagnostic antibodies
- Discovering novel therapies for major human pathogens
- Dissecting host cell invasion by the diarrhoeal pathogen Cryptosporidium
- Epigenetic biomarkers of tuberculosis infection
- Essential role of glycobiology in malaria parasites
- Evolution of haematopoiesis in vertebrates
- Human lung protective immunity to tuberculosis
- Identifying novel treatment options for ovarian carcinosarcoma
- Interaction with Toxoplasma parasites and the brain
- Interactions between tumour cells and their microenvironment in non-small cell lung cancer
- Investigating the role of mutant p53 in cancer
- Microbiome strain-level analysis using long read sequencing
- Minimising rheumatic adverse events of checkpoint inhibitor cancer therapy
- Modelling spatial and demographic heterogeneity of malaria transmission risk
- Naturally acquired immune response to malaria parasites
- Predicting the effect of non-coding structural variants in cancer
- Structural basis of catenin-independent Wnt signalling
- Structure and biology of proteins essential for Toxoplasma parasite invasion
- T lymphocytes: how memories are made
- TICKER: A cell history recorder for longitudinal patient monitoring
- Targeting host pathways to develop new broad-spectrum antiviral drugs
- Targeting post-translational modifications to disrupting the function of secreted proteins
- Targeting the epigenome to rewire pro-allergic T cells
- Targeting the immune microenvironment to treat KRAS-mutant adenocarcinoma
- The E3 ubiquitin ligase Parkin and mitophagy in Parkinson’s disease
- The molecular controls on dendritic cell development
- Understanding malaria infection dynamics
- Understanding the genetics of neutrophil maturation
- Understanding the neuroimmune regulation of innate immunity
- Understanding the proteins that regulate programmed cell death at the molecular level
- Using cutting-edge single cell tools to understand the origins of cancer
- When healthy cells turn bad: how immune responses can transition to lymphoma
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- Renewed support for HIV eradication project
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Andrew Webb - Resources
Researcher:
Systems Biology Mascot Server
Acknowledgements
The Australian Proteomics Computational Facility is funded by the Australian National Health and Medical Research Council (NHMRC grant number 381413), under the Enabling Grant scheme for providing support for a high quality, world-class computational research facility that will enhance the national health and medical research effort.
Access
Access to the Mascot Server at the institute is free to all Australian Academic users.
- To get access to the WEHI Mascot Server, please email apcf@wehi.edu.au. There is no phone support for any Mascot issue.
- For IT issues, i.e. if you can not access the Mascot Server, please ring the IT Help desk and log a fault P +61 3 9345 2589.
Databases
Please note that 7zip or gzip are used to compress the files. You will need a compatible program to decompress them.
MSPnr100
The MSPnr100 is a ~8.9 GByte compressed fasta file compiled from all known reference protein sequences including NCBI, Refseq, UniProt, EuPathDB and Ensembl.
The sequence database is non-redundant at the species level, taxonomy enabled with consistent fasta header lines. A suitable regex for parsing the accession number and description in Mascot is as follows: >[^|]*|\([^|]*\) and >\(.*\) and for Scaffold use >[^\|]*\|([^\|]*) and >(.*)
MSPnr95
The MSPnr95 is a ~7.9 GByte compressed fasta file compiled from the MSPnr100 sequence database at 95% sequence homology at the species level. A suitable regex for parsing the accession number and description in Mascot is as follows: >[^|]*|\([^|]*\) and >\(.*\) and for Scaffold use >[^\|]*\|([^\|]*) and >(.*)
SwissProt
Mascot updates SwissProt automatically on the first of every month, the most recent version is best downloaded directly from other sites. One possible mirror site isftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/
uniprot_sprot.fasta.gz.
If you have the utility wget you can fetch it with:
wget
Contaminants
A file of common contaminants is available. Note that this is different to the default Mascot contaminants database.
Useful tools
Tired of downloading your Mascot results one at a time? Download some handy tools, including a command line submission tool and conversion tools.