The MIPS Ustilago maydis Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis.
Outline of the Project
The underlying Ustilago maydis genome sequence is the first release of the high quality draft sequence of the Broad Institute.
Please note the Broad Institute Disclaimer.
The goal of the MIPS database is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis.
The complete putative gene set of the Broad Institute´s second release is loaded into the database and in addition all deviating putative genes from a putative gene set produced by MIPS with different gene prediction parameters are also loaded.
The complete dataset will then be analysed, gene predictions will be manually corrected due to combined information derived from different gene prediction algorithms and, more important, protein and EST comparisons.
Gene prediction will be restricted to ORFs larger than 50 codons; smaller ORFs will be included only if similarities to other proteins or EST matches confirm their existence or if a coding region was postulated by all prediction programs used.
The resulting proteins will be annotated. They will be classified according to the MIPS classification catalogue receiving appropriate descriptions. All proteins with a known, characterized homolog will be automatically assigned to functional categories using the MIPS functional catalog (FunCat)
All extracted proteins are in addition automatically analysed and annotated by the PEDANT suite.
During the manual analysis procedure gene models and proteins, generated by the Broad Institute, will stay in the database being accessible but indicated as 'not valid', if they are replaced by manually processed models. Links to the corrected models are provided.