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WRKY Genome Analysis in B. juncea
예산
$12,500~$37,500 INR
예상 기간
2~3개월
난이도
전문가
기술 스택
Bioinformatics
Genomics
Comparative Genomics
Phylogenetic Analysis
Sequence Analysis
HMMER
BLAST
OrthoFinder
Python
R
Linux Command Line
Data Visualization
Statistical Analysis
MEME Suite
MCScanX
AI 분석 요약
Brassica juncea의 WRKY 전사 인자 유전자 서열에 대한 포괄적인 인실리코 분석 프로젝트입니다. 유전자 식별, 비교 유전체학, 계통 발생 분석을 핵심으로 하며, 도메인/모티프 분석 및 염색체 위치 분석과 같은 추가 정보도 요구됩니다. 생물정보학, 비교 유전체학, 계통 발생 분석 및 고급 데이터 시각화 역량이 필수적입니다.
프로젝트 원문 설명
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.
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