Required stack
필요 기술
BioinformaticsGenomicsComparative GenomicsPhylogenetic AnalysisSequence AnalysisHMMERBLASTOrthoFinderPythonRLinux Command LineData VisualizationStatistical AnalysisMEME SuiteMCScanX
Project brief
프로젝트 내용
I have assembled the genome-wide WRKY transcription factor sequences for Brassica juncea and now need a complete in-silico analysis focused solely on the gene sequence level. The work must cover three core objectives:
• Identification of all WRKY gene family members present in the current assembly, including accurate locus IDs and coding sequences.
• Comparative genomics that positions each B. juncea WRKY against its orthologues and paralogues in close Brassica relatives and Arabidopsis, highlighting expansions or losses.
• A robust phylogenetic analysis that groups the genes into their canonical WRKY clades with well-supported bootstrap values and a clearly annotated tree ready for publication.
Because I have not fixed a pipeline yet, please recommend the most suitable tools. I am comfortable with you choosing from popular options such as HMMER, Pfam, BLASTp, OrthoFinder, MEGA, IQ-TREE, or any equivalent open-source packages that you feel would produce defendable, reproducible results.
Deliverables will be:
1. A methods report (commands, versions, parameters).
2. Clean FASTA and GFF files for all identified WRKY genes.
3. Comparative genomics tables and synteny plots.
4. Publication-quality phylogenetic tree files (Newick + annotated PDF/PNG).
5. A brief interpretation summary linking the findings to possible functional diversification.
6, chromosomal location
7. domain analysis
8. motif analysis etc.
Please outline the tools you plan to use, an estimated timeline, and any data you need from my side so we can get started quickly.
• Identification of all WRKY gene family members present in the current assembly, including accurate locus IDs and coding sequences.
• Comparative genomics that positions each B. juncea WRKY against its orthologues and paralogues in close Brassica relatives and Arabidopsis, highlighting expansions or losses.
• A robust phylogenetic analysis that groups the genes into their canonical WRKY clades with well-supported bootstrap values and a clearly annotated tree ready for publication.
Because I have not fixed a pipeline yet, please recommend the most suitable tools. I am comfortable with you choosing from popular options such as HMMER, Pfam, BLASTp, OrthoFinder, MEGA, IQ-TREE, or any equivalent open-source packages that you feel would produce defendable, reproducible results.
Deliverables will be:
1. A methods report (commands, versions, parameters).
2. Clean FASTA and GFF files for all identified WRKY genes.
3. Comparative genomics tables and synteny plots.
4. Publication-quality phylogenetic tree files (Newick + annotated PDF/PNG).
5. A brief interpretation summary linking the findings to possible functional diversification.
6, chromosomal location
7. domain analysis
8. motif analysis etc.
Please outline the tools you plan to use, an estimated timeline, and any data you need from my side so we can get started quickly.