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Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

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Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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Next-generation Sequencing

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Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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A Highly Scalable Approach to Perform Ecological Surveys of Selfing Caenorhabditis Nematodes

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959 Nematode Genomes: a semantic wiki for coordinating sequencing projects.

Sujai Kumar¹, Philipp H Schiffer, Mark Blaxter

¹Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3JT, UK.

Nucleic Acids Research

|November 8, 2011

Summary

The 959 Nematode Genomes wiki coordinates global sequencing efforts for nematode genomes. This community-curated platform tracks projects, fostering collaboration among genomicists worldwide.

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Area of Science:

Genomics
Bioinformatics
Community Science

Background:

Second-generation sequencing technologies have democratized genome sequencing.
Metazoan genome sequencing is now accessible to smaller laboratories.
Coordinating distributed sequencing efforts presents a significant challenge.

Purpose of the Study:

To describe the '959 Nematode Genomes' semantic wiki.
To facilitate the collective sequencing of 959 genomes across the phylum Nematoda.
To coordinate and track individual laboratory sequencing projects.

Main Methods:

Utilized a community-curated semantic wiki platform (similar to Wikipedia with semantic extensions).
Implemented machine- and human-readable metadata for querying project status.
Linked species/strain pages to people and organization pages.
Enabled tracking and sharing of preliminary data.

Main Results:

The wiki successfully tracks proposed, in-progress, and completed sequencing projects.
Facilitated the establishment of new international collaborations.
Attracted new researchers to the field of nematode genomics.
Provided a user-friendly platform for data management and sharing.

Conclusions:

The '959 Nematode Genomes' wiki effectively coordinates large-scale, collaborative genome sequencing initiatives.
Semantic wiki technology offers advantages in data management and collaboration over conventional databases.
The platform has fostered a more connected and productive community of nematode genomicists.