_S_P4_cand_genomic
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Short Name: P4_genomes Title: Mealybug genome queries for pheromone biosynthesis genes Description: Survey of the available mealybug genomes for potential sex pheromone biosynthesis genes Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
SEEK ID: https://fairdomhub.org/studies/1039
Projects: SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Contr...
Study position: 5
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Created: 16th May 2022 at 10:27
Last updated: 6th Nov 2024 at 15:25
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https://orcid.org/0000-0003-3644-7827PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
SUSPHIRE aims to provide a sustainable, low-cost biomanufacturing platform for the commercial production of insect pheromones.
Synthetic biology data management spreadsheet: https://fairdomhub.org/data_files/6036
Programme: NIBSys
Public web page: http://susphire.info/susphireproject/
Start date: 1st Apr 2018
End date: 30th Sep 2021
Short Name: T31_mealybug Title: Mealybug genome and transcriptome analyses Description: Searching for enzymes involved in the mealybug pheromone biosynthesis pathways. These pheromones are known to be released by virgin females. Phenodata: ./phenodata_20190523.txt Featuredata: Principal investigator: Heribert Warzecha, Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Studies: Investigation files, _S_P3_expressionEcoli, _S_P4_AdPathGenes, _S_P4_Pcitri_IsoSeq, _S_P4_Pcitri_genome, _S_P4_Pcitri_genome_extSamples, _S_P4_Pcitri_tr1, _S_P4_Pcitri_tr1tr2combo, _S_P4_Pcitri_tr2, _S_P4_cand_all, _S_P4_cand_genomic
Assays: _A_01-CoEXpNetViz_tr2-coexpr, _A_01_NGI-IsoSeq, _A_01_RNAseq-CLC, _A_01_assembly2-rnaSPAdes, _A_01_mapToGenomeAll-STAR, _A_01_renameFASTA-Bioinfo, _A_02-CoEXpNetViz_gen-coexpr, _A_02_CDHIT-Bioinfo, _A_02_assembly2-IPS, _A_02_cDNAcupcake-dry, _A_02_limma-R, _A_02_mapToGenomeAll_limma-R, _A_03-IPS, _A_03_CDHIT2-Bioinfo, _A_03_limma_min50counts-R, _A_03_mapAs2ToGenome-STAR, _A_04_limma_min10counts-R, _A_04_mapIllumina-STAR, _A_04_mapReadsToAs2-STAR, _A_05_As2_tr_limmaDE-R, _A_05_DE_limma-R, _A_05_assembly1-rnaSPAdes, _A_06_assembly1-IPS, _A_07_mapAs1ToGenome-STAR, _A_08_mapReadsToAs1-STAR, _A_09_As1_tr_limmaDE-R, _A_C98F-EcoliExpr, _A_IDIsearch-Bioinfo, _A_IPS-bioinfo, _A_MAST-bioinfo, _A_MEME-bioinfo, _A_MSA-bioinfo, _A_MeUppS-EcoliExpr, _A_Node14610-EcoliExpr, _A_Node14610DmTP-EcoliExpr, _A_OtherMealybugCandidates-Alignment, _A_Pc1599-EcoliExpr, _A_Pc23180-EcoliExpr, _A_Pc2704-EcoliExpr, _A_Pc32607-EcoliExpr, _A_Pc7366II-EcoliExpr, _A_PcCis24-EcoliExpr, _A_Strep_CLDS-bioinfo, _A_TPS_phy-bioinfo, _A_Terzyme-bioinfo, _A_Trans1153-EcoliExpr, _A_Trans2-EcoliExpr, _A_Trans39-EcoliExpr, _A_Trans57-EcoliExpr, _A_Trans64-EcoliExpr, _A_Trans94-EcoliExpr, _A_candidatemining-bioinfo, _A_g14825_recon-bioinfo, _A_smallIDSsubunit-motifs, _I_T31_mealybug-files, _S_P3_expressionEcoli-files, _S_P4_AdPathGenes-files, _S_P4_Pcitri_IsoSeq-files, _S_P4_Pcitri_genome-files, _S_P4_Pcitri_genome_extSamples-files, _S_P4_Pcitri_tr1-files, _S_P4_Pcitri_tr1tr2combo-files, _S_P4_Pcitri_tr2-files, _S_P4_cand_all-files, _S_P4_cand_genomic-files
Files connected to study: _S_P4_cand_genomic
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T31_mealybug
Study: _S_P4_cand_genomic
Short Name: g14825_recon-bioinfo Assay Class: DRY Assay Type: bioinfo Title: TPS gene g14825 reconstruction Description: Reconstruction of g14825 exon structure by checking RNA-seq mapped reads vs the genome-predicted gene model pISA Assay creation date: 2018-11-23 pISA Assay creator: MPE Phenodata: ../../phenodata_20181003.txt Data: /FITO_ws/markop/pcitri_bam Genome reference files: ../../_S_P4_Pcitri_tr/_A_RNAseq-CLC/input/
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T31_mealybug
Study: _S_P4_cand_genomic
Short Name: IPS-bioinfo Assay Class: DRY Assay Type: bioinfo Title: InterProScan results analysis Description: Anaylsis of IPS results pISA Assay creation date: 2018-11-23 pISA Assay creator: MPE Phenodata: None Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T31_mealybug
Study: _S_P4_cand_genomic
Short Name: MAST-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Search for MEME motif in proteome of P. citri Description: Using MEME software to look for motifs in proteins that resemble those found in plants producing similar compounds to mealybug sex pheromones pISA Assay creation date: 2018-11-23 pISA Assay creator: MPE Phenodata: None Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T31_mealybug
Study: _S_P4_cand_genomic
Short Name: MEME-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Finding motifs in candidate protein sequences using MEME Description: Using MEME software to look for motifs in proteins that resemble those found in plants producing similar compounds to mealybug sex pheromones pISA Assay creation date: 2018-11-23 pISA Assay creator: MPE Phenodata: None Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T31_mealybug
Study: _S_P4_cand_genomic
Short Name: Terzyme-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Terzyme analysis Description: Terzyme is a predictive algorithm for identification, classification and assignment of broad substrate unit to terpene synthase (TPS) and prenyl transferase (PT) enzymes. Data: pISA Assay creation date: 2018-11-23 pISA Assay creator: MPE Phenodata: None Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T31_mealybug
Study: _S_P4_cand_genomic
Short Name: TPS_phy-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Terpene synthases phylogeny Description: Philogenetica analysis with ClustalOmega and Phylogeny.fr web service pipeline pISA Assay creation date: 2018-11-23 pISA Assay creator: MPE Phenodata: None Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T31_mealybug
Study: _S_P4_cand_genomic
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_TPS_phy-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_Terzyme-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_MEME-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_Terzyme-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_Terzyme-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_MEME-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_MAST-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_MEME-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_IPS-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_IPS-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_MAST-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_g14825_recon-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_IPS-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_g14825_recon-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_g14825_recon-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_g14825_recon-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_TPS_phy-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_TPS_phy-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_TPS_phy-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_TPS_phy-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_TPS_phy-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_TPS_phy-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_TPS_phy-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_TPS_phy-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_TPS_phy-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_MAST-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_MAST-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_MAST-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_MAST-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_MEME-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_Terzyme-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_TPS_phy-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_IPS-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_MAST-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_MEME-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_genomic/_A_MEME-bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
