Bioinfomatics: Difference between revisions
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== Detailed Explanation == | == Detailed Explanation == | ||
== Bioinfomatics == | |||
A combined technologies with biology, computer science, mathmatics and statistics. <ref>https://www.youtube.com/watch?v=ky1-mF0fHnQ</ref> | A combined technologies with biology, computer science, mathmatics and statistics. <ref>https://www.youtube.com/watch?v=ky1-mF0fHnQ</ref> | ||
Bioinfomatics workflow steps | Bioinfomatics workflow steps | ||
# quality control assessmemt steps | # quality control assessmemt steps | ||
# sequence alignment | # sequence alignment | ||
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# statistical comparisons | # statistical comparisons | ||
# mutltiomic ingetration | # mutltiomic ingetration | ||
== Bioinfomatics curated software list<ref>https://github.com/danielecook/Awesome-Bioinformatics</ref> == | |||
* Package suites | * Package suites | ||
* Data Tools | * Data Tools | ||
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** Data Analysis | ** Data Analysis | ||
** Sequence Alignment | ** Sequence Alignment | ||
*** Pairwise | |||
*** Multiple Sequence Alignment | |||
*** Clustering | |||
** Quantification | |||
** Variant Calling | |||
*** Structural variant callers | |||
** BAM File Utilities | |||
** VCF File Utilities | |||
** GFF BED File Utilities | |||
** Variant Simulation | |||
** Variant Prediction/Annotation | |||
* Tools for Assessment of Variants | |||
** [http://genetics.bwh.harvard.edu/pph2/ PolyPhen-2] is a tool for predicting the effect of an amino acid substitution on protein structure and function, based on comparative genomics and experimentally determined protein structures. It is available as a web service, and can also be downloaded as a standalone application. | |||
** [http://genetics.bwh.harvard.edu/snptrack SNPtrack] is a simple interface for mutation mapping and identifying causal mutations from whole-genome sequencing studies. It is available as a web service. | |||
* Tools for Mass Spectrometry and Proteomics | |||
** [http://genetics.bwh.harvard.edu/msblast MS-BLAST] is a tool for searching protein sequences identified with tandem mass spectrometry against databases of protein sequences. It is available as a web service and as a standalone software. | |||
* Tools for Statistical Genetics | |||
** [https://sunyaevlab.hms.harvard.edu/wiki/!web/jlim Joint Likelihood Mapping (JLIM)] is a tool to [[test]] for shared genetic effect between two genetic association data, for example, a disease GWAS study and gene expression QTL (eQTL) study. | |||
** [https://sunyaevlab.hms.harvard.edu/wiki/!web/jlim2.0 Joint Likelihood Mapping 2 (JLIM_2.0)] is a version of JLIM which supports meta-analysis across more than one cohort of matching ancestry. | |||
** [https://sunyaevlab.hms.harvard.edu/wiki/!web/jlim2.5 Joint Likelihood Mapping (JLIM) 2.5] is a new version of JLIM based on summary statistics. | |||
** [http://github.com/sgchun/nps NPS] is a tool for polygenic risk scoring based on partitioning-based non-parametric shrinkage algorithm. | |||
** [https://github.com/snz20/RVTT RVTT] is a novel statistical test of trend that assesses the relationship of the frequency of qualifying rare variants in a pathway with dichotomous disease phenotypes leveraging the Cochran-Armitage test statistic. | |||
* Tools for Cancer Genomics | |||
** [https://www.genepattern.org/modules/docs/MutPanning#gsc.tab=0 MutPanning] is designed to detect rare cancer driver genes from aggregated | |||
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Revision as of 15:28, 16 July 2026
Overview
Bioinfomatics에 대한 기술 문서입니다.
Summary
- 무엇인가? - Bioinfomatics
- 왜 필요한가? - HPC 및 서버 환경에서 필수 개념
- 언제 사용하는가? - 서버 구성, 성능 튜닝, 문제 해결 시
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Purpose
이 문서가 존재하는 이유
- Goal: Bioinfomatics에 대한 기술 정보 제공
- Scope: Bioinfomatics의 개념, 사용법, 설정
- Non-goals: 다른 주제로의 확장
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Key Concepts
| Concept | Description | Related |
|---|---|---|
| Bioinfomatics | HPC/서버 환경에서 중요한 기술 개념 | Linux, Server |
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Detailed Explanation
Bioinfomatics
A combined technologies with biology, computer science, mathmatics and statistics. [1]
Bioinfomatics workflow steps
- quality control assessmemt steps
- sequence alignment
- data summarization into genes/regions
- data annotation to genomics features
- statistical comparisons
- mutltiomic ingetration
Bioinfomatics curated software list[2]
- Package suites
- Data Tools
- Downloading
- Compressing
- Data Processing
- Command Line Utilities
- Next Generation Sequencing
- Workflow Managers
- Pipelines
- Sequence Processing
- Data Analysis
- Sequence Alignment
- Pairwise
- Multiple Sequence Alignment
- Clustering
- Quantification
- Variant Calling
- Structural variant callers
- BAM File Utilities
- VCF File Utilities
- GFF BED File Utilities
- Variant Simulation
- Variant Prediction/Annotation
- Tools for Assessment of Variants
- PolyPhen-2 is a tool for predicting the effect of an amino acid substitution on protein structure and function, based on comparative genomics and experimentally determined protein structures. It is available as a web service, and can also be downloaded as a standalone application.
- SNPtrack is a simple interface for mutation mapping and identifying causal mutations from whole-genome sequencing studies. It is available as a web service.
- Tools for Mass Spectrometry and Proteomics
- MS-BLAST is a tool for searching protein sequences identified with tandem mass spectrometry against databases of protein sequences. It is available as a web service and as a standalone software.
- Tools for Statistical Genetics
- Joint Likelihood Mapping (JLIM) is a tool to test for shared genetic effect between two genetic association data, for example, a disease GWAS study and gene expression QTL (eQTL) study.
- Joint Likelihood Mapping 2 (JLIM_2.0) is a version of JLIM which supports meta-analysis across more than one cohort of matching ancestry.
- Joint Likelihood Mapping (JLIM) 2.5 is a new version of JLIM based on summary statistics.
- NPS is a tool for polygenic risk scoring based on partitioning-based non-parametric shrinkage algorithm.
- RVTT is a novel statistical test of trend that assesses the relationship of the frequency of qualifying rare variants in a pathway with dichotomous disease phenotypes leveraging the Cochran-Armitage test statistic.
- Tools for Cancer Genomics
- MutPanning is designed to detect rare cancer driver genes from aggregated
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Best Practices
- 최신 버전 사용 권장
- 공식 문서 참고
- 테스트 환경에서 먼저 검증
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References
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Related Pages
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