User:Jose Fabricio Lopez/Notebook/GEDF/2012/09/12

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Contents

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.
  • Run prediction Augustus with both set.

Things done

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

Loogbook

BLAST btwn t.at.both vs ncrna
  • 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

Augus pred vs TrichodermaFrozen
  • 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

BLAST e-value 1e-3

In order to get more hits I run blast again. e-value 1e-3. It is made just in case. Between Agustus predicted and T.at.v2.aa

JGI ESTs trainning

Training job ID: train7t4v7v8r


Species name: Trichoderma_atroviride.JGI

Genome file: Trichoderma_atroviride_v2.fasta

Training gene structure file: Tatroviridev2_FrozenGeneCatalog_20100319.gff

Prediction of 0bp away

Made with parameters given by training. With personal isotigs.fna Submitting

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

Results


Wed Sep 12 22:28:30 CEST 2012 - Message:


Details of your job:

Prediction job ID: predds5qadkd

Parameter archive: parameters.tar.gz

Genome file: IntergenicFasta.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

Augustus BOTH set

Submitting


Sep 13 00:01:40 CEST 2012 - Message:

Details of your job:


Prediction job ID: predKmQCPAiD

Parameter archive: parameters.tar.gz

Genome file: RealIntergenicBOTH.fas

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

Results


Thu Sep 13 00:01:40 CEST 2012 - Message:


Details of your job:


Prediction job ID: predKmQCPAiD

Parameter archive: parameters.tar.gz

Genome file: RealIntergenicBOTH.fas

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


Your AUGUSTUS prediction job predKmQCPAiD finished.

Extras

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