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

From OpenWetWare
Jump to navigationJump to search
Line 19: Line 19:
*Run BLAST of Augus vsTrichodermaFrozen with less e-value.
*Run BLAST of Augus vsTrichodermaFrozen with less e-value.
*Training Agusutus with JGI ESTs.
*Training Agusutus with JGI ESTs.
*Run prediction Augustus with 0bp away gene set.


====Things done====
====Things done====

Revision as of 13:14, 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
<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>

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.

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
Retrieved from "https://openwetware.org/mediawiki/index.php?title=User:Jose_Fabricio_Lopez/Notebook/GEDF/2012/09/12&oldid=625642"