Assays

Short Name: IDIsearch-Bioinfo Assay Class: DRY Assay Type: Bioinfo Title: Search of IDI candidates from Pcitri sequences Description: Identifying isopentenyl isomerase candidate genes from genomic and transcriptomic sequences of Pcitri. pISA Assay creation date: 2021-12-31 pISA Assay creator: Mojca Jutersek Phenodata: None Featuredata: Data:

Short Name: MSA-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Multiple sequence alignment of cis and trans candidate IDS Description: MSA and phylogenetic analysis of candidates in MEGA pISA Assay creation date: 2019-06-05 pISA Assay creator: Mojca Jutersek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Short Name: OtherMealybugCandidates-Alignment Assay Class: DRY Assay Type: Alignment Title: Alignment of other mealybug candidate enzymes Description: We created alignments and phylogenetic trees of P. citri IDS candidates with IDS homologs mined from the genomes of two other species: Planococcus ficus and Planococcus longispinus, to determine which of the candidates are evolutionarily conserved and their phylogenetic relationships among the three species. pISA Assay creation date: 2021-03-02 ...

Short Name: smallIDSsubunit-motifs Assay Class: DRY Assay Type: motifs Title: Search for P. citri homologs of small IDS subunits Description: Since in plants, some IDS enzymes require a small non-catalytical subunit for their functioning, we decided to determine, whether we could find homologs of such proteins in P. citri sequences and test them in combination with IDS candidates. We performed a motif search in the P.citri proteome. pISA Assay creation date: 2021-04-13 pISA Assay creator: MJU ...

Short Name: Strep_CLDS-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Search for Streptomyces CLDS homologue in the generated transcriptomes of P. citri Description: Using BLAST to seqrch for homologues of Streptomyces Cyclolavandulyl diphosphate synthase in P. citri transsctiptome tr1 and tr2 pISA Assay creation date: 2019-12-30 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20181003.txt Featuredata: Data:

Files connected to study: _S_P4_cand_all

Short Name: candidatemining-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Mining of IDS homologues from genome and de novo transcriptomes of P. citri Description: We selected homologues of cis and trans IDS enzymes in P. citri genome and both versions of the de novo transcriptome. Selection was done based on IPRscan results. pISA Assay creation date: 2019-06-05 pISA Assay creator: Mojca Jutersek Phenodata: ../../phenodata_20190523.txt Featuredata: Data: