Bioinfomatics: Difference between revisions

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* Package suites
* Package suites
* Data Tools
* Data Tools
** Downloading
Downloading
** Compressing
Compressing
* Data Processing
* Data Processing
** Command Line Utilities
Command Line Utilities
* Next Generation Sequencing
* Next Generation Sequencing
** Workflow Managers
Workflow Managers
** Pipelines
Pipelines
** Sequence Processing
Sequence Processing
** Data Analysis
Data Analysis
** Sequence Alignment
Sequence Alignment
*** Pairwise
*** Pairwise
*** Multiple Sequence Alignment
*** Multiple Sequence Alignment
*** Clustering
*** Clustering
** Quantification
Quantification
** Variant Calling
Variant Calling
*** Structural variant callers
*** Structural variant callers
** BAM File Utilities
BAM File Utilities
** VCF File Utilities
VCF File Utilities
** GFF BED File Utilities
GFF BED File Utilities
** Variant Simulation
Variant Simulation
** Variant Prediction/Annotation
Variant Prediction/Annotation
* Tools for Assessment of Variants
* 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/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.  
[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  
* 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.  
[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
* 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/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/jlim2.0 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.
[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.
[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.  
[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
* 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
[https://www.genepattern.org/modules/docs/MutPanning#gsc.tab=0 MutPanning] is designed to detect rare cancer driver genes from aggregated


== Best Practices ==
== Best Practices ==

Latest revision as of 13:57, 2 October 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

Purpose

이 문서가 존재하는 이유

  • Goal: Bioinfomatics에 대한 기술 정보 제공
  • Scope: Bioinfomatics의 개념, 사용법, 설정
  • Non-goals: 다른 주제로의 확장

Key Concepts

Concept Description Related
Bioinfomatics HPC/서버 환경에서 중요한 기술 개념 Linux, Server

Detailed Explanation

Bioinfomatics

A combined technologies with biology, computer science, mathmatics and statistics. [1]

Bioinfomatics workflow steps

  1. quality control assessmemt steps
  2. sequence alignment
  3. data summarization into genes/regions
  4. data annotation to genomics features
  5. statistical comparisons
  6. 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

Best Practices

  • 최신 버전 사용 권장
  • 공식 문서 참고
  • 테스트 환경에서 먼저 검증

References

Related Pages

Knowledge Graph

Related

→ Linux → Server → Hardware → Network

  1. ↑ https://www.youtube.com/watch?v=ky1-mF0fHnQ
  2. ↑ https://github.com/danielecook/Awesome-Bioinformatics
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