User:Jose Fabricio Lopez/Notebook/GEDF/2012/09/12: Difference between revisions

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*Prediction of 0bp away.
*Prediction of 0bp away.
<code>
Prediction job ID: predds5qadkd
Prediction job ID: predds5qadkd
Parameter archive: parameters.tar.gz
Parameter archive: parameters.tar.gz
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Allowed gene structure: predict any number of (possibly partial) genes
Allowed gene structure: predict any number of (possibly partial) genes
Ignore conflictes with other strand: false
Ignore conflictes with other strand: false
</code>


==Extras==
==Extras==


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Revision as of 13:17, 12 September 2012

Gene Expression and Development in Fungi <html><img src="http://openwetware.org/images/9/94/Report.png" border="0" /></html> Main project page
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Trichoderma & P. vulgaris interaction

Things to do

Things done

Loogbook

Intergenic sequences in T.atroviride

Things to do

  • Check BLAST btwn t.at.both vs ncrna.
  • Analyze results from Augus pred vs TrichodermaFrozen.
  • Run BLAST of Augus vsTrichodermaFrozen with less e-value.
  • Training Agusutus with JGI ESTs.
  • Run prediction Augustus with 0bp away gene set.

Things done

  • Checked BLAST btwn t.at.both vs ncrna.
  • Analyzing
  • Running
  • Job submitted and running.
  • 0bp away gene set. Job submitted

Loogbook

  • No hits found in BLAST btwn t.at.both vs ncrna.

-evalue 1e-3 -num_alignments 10 -query RealIntergenicBOTH.fas -out BLASTnTotalIntergenicRegionsVsncrnaDB.txt -word_size 4 -outfmt 6

  • 13538 hits found.
    • 9326 100% of identity.
    • 5778 of e-value
    • 9694 uniq names with hit this means predicted almost.
  • Sesibility= .78

TrichodermaAtrovirideV2.aa -evalue 1e-5 -num_alignments 1 -query augustusPredictionTestResults.aa -out BLASTTestAugustusVsTrichodremaFrozenGene.txt -word_size 7 -outfmt 6

In order to get more hits I run blast again. e-value 1e-3. It is made just in case.

  • Prediction of 0bp away.

Prediction job ID: predds5qadkd Parameter archive: parameters.tar.gz Genome file: ****Fasta.fna User set UTR prediction: false Report genes on: both strands Alternative transcripts: none Allowed gene structure: predict any number of (possibly partial) genes Ignore conflictes with other strand: false

Extras
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