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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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,...
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Comparing Copy Number Variations and SNPs02:26

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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.
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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Principles of Pharmacogenetics: Types of Genetic Variants01:27

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The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
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Conservation of Protein Domains Over Different Proteins02:26

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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dbSAP: single amino-acid polymorphism database for protein variation detection.

Ruifang Cao1, Yan Shi1, Shuangguan Chen1

  • 1The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.

Nucleic Acids Research
|December 2, 2016
PubMed
Summary
This summary is machine-generated.

This study introduces dbSAP, a comprehensive database for single amino-acid polymorphisms (SAPs). dbSAP integrates extensive data on SAPs, peptides, and spectra to aid research into human traits and diseases.

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Area of Science:

  • Genomics and Proteomics
  • Human Genetics
  • Bioinformatics

Background:

  • Millions of human single nucleotide polymorphisms (SNPs) are known, potentially influencing traits and diseases.
  • Non-synonymous SNPs lead to single amino-acid polymorphisms (SAPs), but their study is limited by incomplete databases and low mass spectrometry (MS) coverage.

Purpose of the Study:

  • To present dbSAP, a comprehensive database for accessing information on single amino-acid polymorphisms (SAPs).
  • To facilitate the exploration of human SAPs and their associations with genes, pathways, diseases, and drug targets.

Main Methods:

  • Constructed a customized protein database by integrating and annotating human SNPs and mutations from eight major databases.
  • Applied rigorous quality control measures to the integrated data.
  • Analyzed large-scale mass spectrometry (MS) datasets from diverse human tissues and cell lines.

Main Results:

  • Identified a total of 16,854 single amino-acid polymorphism (SAP) peptides.
  • Associated these SAP peptides with 439,537 spectra.
  • Developed the dbSAP database for convenient access to comprehensive SAP-related information.

Conclusions:

  • dbSAP provides a valuable resource for researchers studying human genetic variation and its impact on health.
  • The database enhances the understanding of single amino-acid polymorphisms (SAPs) and their functional consequences.
  • dbSAP is freely accessible online, promoting further research in the field.