Related Experiment Video
Updated: May 5, 2026
09:34
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
36.1K
snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing
BMC Bioinformatics
|November 20, 2013
Summary
This study introduces snp-search, a tool simplifying bacterial pathogen genome analysis. It efficiently manages single nucleotide polymorphism (SNP) data, making complex genomic information accessible for hypothesis testing.
Area of Science:
- Genomics
- Bioinformatics
- Microbial Pathogenesis
Background:
- Bacterial pathogen genome mapping generates thousands of single nucleotide polymorphisms (SNPs).
- Interpreting large SNP datasets from flat files is complex and challenging.
- A database solution is needed for simplified SNP interrogation and comprehensible output.
Purpose of the Study:
- To present snp-search, a novel tool for managing and analyzing SNP data.
- To facilitate easier manipulation and searching of complex SNP datasets.
- To enable comprehensible output for genomic research.
Main Methods:
- Development of the snp-search tool.
- Creation of a SNP database from Variant Call Format (VCF) files.
- Implementation of query functions for data manipulation and analysis.
Main Results:
- snp-search manages SNP data, enabling conversion to FASTA sequences.
- The tool facilitates phylogenetic tree construction and identification of unique SNPs.
- Contextual SNP information and phenotype associations can be queried.
Conclusions:
- snp-search effectively manages SNP data for bacterial pathogen genome analysis.
- The tool provides useful outputs for testing significant biological hypotheses.
- Facilitates easier interpretation of complex genomic data.
Related Concept Videos
01:05Single Nucleotide Polymorphisms-SNPs
14.8K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
14.8K
02:26Comparing Copy Number Variations and SNPs
11.6K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
11.6K
03:21RNA-seq
9.4K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.4K