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
Submission
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
hu 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
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