Bioinfomatics

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

Bioinfomatics

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

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

• 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

• Bioinfomatics

Related Pages

• Linux
• Server
• Hardware
• Network

Knowledge Graph

Related

→ Linux → Server → Hardware → Network