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Genomic Insights: Unveiling Prokaryotic SSR Diversity

A specialized database offering a comprehensive collection of polymorphic simple sequence repeats, crucial for advanced prokaryotic genomic research and understanding genetic variation.

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What is PSSRdb?

A Specialized Bioinformatics Resource

The Polymorphic Simple Sequence Repeats database (PSSRdb) stands as a dedicated bioinformatics resource. Its core mission is to systematically catalog and present polymorphic simple sequence repeats (SSRs) that have been meticulously identified and extracted from a diverse array of prokaryotic genomes.

Unlocking Prokaryotic Genetic Variation

PSSRdb serves as an indispensable tool for researchers delving into the intricacies of genetic variation and the evolutionary dynamics within prokaryotic organisms. By centralizing data on these variable genetic markers, it facilitates advanced studies in microbial genomics, population genetics, and molecular epidemiology.

Core Content & Focus

Prokaryotic Exclusivity

This database is exclusively focused on prokaryotic organisms. This targeted approach ensures a high degree of relevance and specificity for studies concerning bacteria and archaea, which exhibit unique genomic characteristics and evolutionary pressures compared to eukaryotes.

Simple Sequence Repeats (SSRs)

PSSRdb is populated with Simple Sequence Repeats (SSRs), also widely recognized as microsatellites. These are short, tandemly repeated DNA sequences, typically comprising 1-6 base pairs, which are repeated multiple times throughout a genome. Their repetitive nature makes them prone to replication slippage, leading to length variations.

Emphasizing Polymorphism

A critical feature of PSSRdb is its emphasis on the *polymorphic* nature of these SSRs. Polymorphism, in this context, refers to the variation in the number of repeat units among different strains, isolates, or individuals of a prokaryotic species. Such length variations render SSRs exceptionally valuable as genetic markers for distinguishing between closely related organisms.

Fundamental Concepts

Understanding SSRs and Polymorphism

To fully appreciate the utility of PSSRdb, a foundational understanding of Simple Sequence Repeats (SSRs) and genetic polymorphism is essential for Master's level students in genomics and bioinformatics.

Simple Sequence Repeats (SSRs)

SSRs are stretches of DNA consisting of short nucleotide motifs (e.g., AT, GATA) repeated in tandem. These regions are highly mutable due to errors during DNA replication, specifically 'replication slippage,' where the DNA polymerase can add or remove repeat units. This leads to variations in the total length of the SSR locus.

Genetic Polymorphism

Polymorphism refers to the existence of multiple alleles (variant forms of a gene or DNA sequence) within a population. For SSRs, polymorphism is typically observed as differences in the number of repeat units at a specific genomic location. These length variations are inherited and can be used to differentiate individuals or strains.

Significance in Prokaryotes

In prokaryotic genomics, polymorphic SSRs are particularly significant for several reasons:

  • Strain Typing: They provide highly discriminatory markers for identifying and differentiating between bacterial or archaeal strains, crucial for epidemiological studies and outbreak investigations.
  • Phylogenetic Analysis: Variations in SSRs can shed light on evolutionary relationships and population structures within prokaryotic species.
  • Gene Regulation: Some SSRs located within coding or regulatory regions can influence gene expression, leading to rapid phenotypic changes, such as phase variation in virulence factors, allowing prokaryotes to adapt quickly to changing environments.
  • Genetic Mapping: They serve as valuable markers for genetic mapping studies, helping to locate genes associated with specific traits.

Genesis & Authorship

Inception and Release

PSSRdb was officially released in 2010, marking a significant contribution to the field of prokaryotic genomics. Its development addressed a growing need for a specialized repository of polymorphic simple sequence repeats, providing a focused resource for the scientific community.

Key Author

The primary author credited for the development of PSSRdb is Pankaj Kumar. His work, alongside collaborators, was instrumental in conceptualizing and implementing this valuable bioinformatics tool.

Institutional Backing

The database was developed within the Laboratory of Computational Biology India, a research group affiliated with the esteemed Centre for DNA Fingerprinting and Diagnostics (CDFD). CDFD is a leading institution in India dedicated to cutting-edge research in DNA fingerprinting, diagnostics, and computational biology, providing a robust scientific environment for such initiatives.

Access & Utility

Online Accessibility

PSSRdb is made available to the global scientific community through a dedicated online platform. Researchers can access the database via its official website, providing a centralized and user-friendly interface for querying and retrieving data on prokaryotic polymorphic SSRs.

Research Facilitation

The primary utility of PSSRdb lies in its ability to facilitate a wide range of genomic studies. By providing curated data on polymorphic SSRs, it empowers researchers to:

  • Conduct detailed analyses of genetic diversity within prokaryotic populations.
  • Investigate evolutionary relationships and phylogenetic patterns.
  • Develop molecular markers for strain identification and epidemiological tracking.
  • Explore the functional implications of SSR variation in prokaryotic biology.

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References

References

A full list of references for this article are available at the Polymorphic simple sequence repeats database Wikipedia page

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Disclaimer

Important Notice

This page was generated by an Artificial Intelligence and is intended for informational and educational purposes only. The content is based on a snapshot of publicly available data from Wikipedia and may not be entirely accurate, complete, or up-to-date.

This is not professional scientific advice. The information provided on this website is not a substitute for consulting original scientific literature, official database documentation, or seeking advice from qualified bioinformatics specialists or geneticists. Always refer to primary research articles and official resources for specific scientific inquiries or project needs. Never disregard professional scientific guidance because of something you have read on this website.

The creators of this page are not responsible for any errors or omissions, or for any actions taken based on the information provided herein.