Genome Annotation and Effector Prediction for Phytophthora sorghi
Corresponding Organization : University of California, Davis
Other organizations : United States Department of Agriculture, Texas A&M University
Variable analysis
- Use of RepeatModeler v1.73 to define repeats in the genome assembly of P. sorghi
- Use of RepeatMasker v4.0.9 to mask repeats in the genome assembly of P. sorghi
- Use of the same repeat library to identify repeats in the transcriptome assembly
- Use of MAKER to annotate gene models in the genome assembly
- Use of hidden Markov models (HMM) with HMMER and regular expression string searches to identify additional putative effectors
- Provision of the RepeatModeler profile, assembled transcripts, translated ORFs from the transcriptome of P. sorghi, ESTs, and protein sequences of other oomycete species to the MAKER pipeline
- Initial run of MAKER without a SNAP HMM, inferring genes using est2genome and protein2genome
- Training of a SNAP HMM using the initial MAKER predictions, and subsequent runs of MAKER using both est2genome and protein2genome set to 0
- Repeated training of new SNAP HMMs and running of MAKER to generate three SNAP HMMs
- Evaluation of the annotations produced to select a single optimal run
- Annotation of genes encoding putative effectors, including use of SignalP, HMMs for CRN motifs, and searches for RXLR and EER motifs
- Reconciliation of the putative effectors and MAKER annotations
- Number of gene models predicted
- Mean protein length
- BLASTp hits to other oomycete annotations
- Pfam domains annotated by InterProScan
- Number of high-confidence putative effectors (HCPEs) and low-confidence putative effectors (LCPEs)
- Use of the RepeatModeler profile, assembled transcripts, translated ORFs from the transcriptome of P. sorghi, ESTs, and protein sequences of other oomycete species as input for the MAKER pipeline
Annotations
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