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Genome sequences and databases

   

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     GnpIs give access to several databases of organisms and biological information using a simple but powerfull form.
     L. maculans structural and functional annotation databases have been indexed and pertinent matches found are directly linked to the corresponding GnpGenome or Genome Report System.
     Special terms are authorized and results obtain with "membrane" are not equal to "*membrane*".
     For more information on queries, see the associated documentation.
  •   BLAST and extract sequences with Extract-nuc (nucleic sequences) and Extract-prot (protein sequences): : Available blasts are: blastn, tblastn,blastp
     - Supercontigs (41 seqs) and contigs (1698 seqs) v2
     - Genes and protein predicted
     - L maculans ESTs v6 (42222 seqs) and EST contigs
  •   Genome Report System : A report system to gather all information available (structural & functional) related to genes predicted
  •   GnpGenome : a Genome Browser for Lmaculans Structural annotation : A database based on the chado model (GMOD) gathers all the information produced the structural annotation pipeline of L. maculans genome.
    • Prediction pipeline has been processed through ab initio gene finding softwares and similarity methods. All results have been then gathered and processed by Eugene to predict 12,469 gene models > 100 bases. The gene models were separated into two subsets: one main set comprising 11,561 genes with coding sequence > 300 bases, or < 300 bases but with at least one EST evidence or domain/motif evidence (as provided by the InterProScan analysis); and a second subset of 908 more dubious genes with a coding sequence smaller than 300 bases and without any EST or domain/motif support.
    • 249 tRNAs predicted by tRNAscan-SE
    • Protein mapping from Uniprot and a Fungal protein database (containing proteins from 30 fungal genomes)
    • Bac End Sequences mapping (23026 sequences)
    • ESTs (42222) and EST contigs (6186 unisequences) from 15 L. maculans cDNA libraries
    • Genes from Stagonospora nodorum (JGI)
    • Transposable Elements copies from Consensus families (REPET TEdenovo manually curated and used to annotates genome (TEannot)
    • AT regions manually annotated
    • SSRs and low complexity region provided by RepeatMasker
Update: 13 Aug 2015
Creation date: 10 Dec 2010