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

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*Check BLAST btwn t.at.both vs ncrna.
*Check BLAST btwn t.at.both vs ncrna.
*Analyze results from Augus pred vs TrichodermaFrozen.
*Analyze results from Augus pred vs TrichodermaFrozen.
 
*Run BLAST of Augus vsTrichodermaFrozen with less e-value.
*Training Agusutus with JGI ESTs.
====Things done====
====Things done====
*Checked BLAST btwn t.at.both vs ncrna.
*Checked BLAST btwn t.at.both vs ncrna.
*Analyzing
*Analyzing
*Running
*Job submitted and running.
===Loogbook===
===Loogbook===
*No hits found in BLAST btwn t.at.both vs ncrna.
*No hits found in BLAST btwn t.at.both vs ncrna.
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TrichodermaAtrovirideV2.aa -evalue 1e-5 -num_alignments 1 -query augustusPredictionTestResults.aa -out BLASTTestAugustusVsTrichodremaFrozenGene.txt -word_size 7 -outfmt 6
TrichodermaAtrovirideV2.aa -evalue 1e-5 -num_alignments 1 -query augustusPredictionTestResults.aa -out BLASTTestAugustusVsTrichodremaFrozenGene.txt -word_size 7 -outfmt 6
</code>
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In order to get more hits I run blast again. e-value 1e-3. It is made just in case.
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==Extras==
==Extras==


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Revision as of 11:53, 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.

Things done

  • Checked BLAST btwn t.at.both vs ncrna.
  • Analyzing
  • Running
  • Job submitted and running.

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.

Extras
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