News/GMOD Paper Cuts, Dec 6th, 2013

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GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system [1]

Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates.

A fascinating insight into the biology and genome of the king cobra; the Burmese python has also been recently been sequenced [2], with both projects using MAKER for automated annotation.

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools [3]

PortEco aims to collect, curate and provide data and analysis tools to support basic biological research in Escherichia coli (and eventually other bacterial systems). PortEco is implemented as a 'virtual' model organism database that provides a single unified interface to the user, while integrating information from a variety of sources.

PortEco integrates E. coli data from numerous sources and uses a wiki-based system to enable collaborative knowledge management. PortEco is currently testing a JBrowse installation with the view to migrating over to JBrowse from their current GBrowse sequence browser.

The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse [4]

The Mouse Genome Database (MGD) is the community model organism database resource for the laboratory mouse, a premier animal model for the study of genetic and genomic systems relevant to human biology and disease. MGD maintains a comprehensive catalog of genes, functional RNAs and other genome features as well as heritable phenotypes and quantitative trait loci.

An update on the resources available at Mouse Genome Database (MGD), one of the groups involved in GMOD since the very beginning of the project.

NECTAR: a database of codon-centric missense variant annotations [5]

NECTAR (Non-synonymous Enriched Coding muTation ARchive) is a database and web application to annotate disease-related and functionally important amino acids in human proteins.

This stylishly-designed website draws data on disease mutations from numerous sources, including Ensembl, HGMD-PUBLIC, UniProt, COSMIC, and ClinVar, and includes GBrowse-able disease variants, function annotations, and paralogue annotations and a DAS server. Sweet!

Identification of a 31-bp Deletion in the RELN Gene Causing Lissencephaly with Cerebellar Hypoplasia in Sheep [6]

Lissencephaly is an inherited developmental disorder in which neuronal migration is impaired. A type of lissencephaly associated with cerebellar hypoplasia (LCH) was diagnosed in a commercial flock of Spanish Churra sheep. The genotyping of 7 affected animals and 33 controls with the OvineSNP50 BeadChip enabled the localization of the causative mutation for ovine LCH to a 4.8-Mb interval on sheep chromosome 4 using genome-wide association and homozygosity mapping.

Tracking down a sequence variation that causes developmental problems in sheep: a nice combination of classical genetics (studying families trees and examining phenotypes) and modern techniques, using resources provided at CSIRO's Livestock Genomics website.

Happy reading!

  1. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1073.2Fpnas.1314702110
  2. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1073.2Fpnas.1314475110
  3. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1093.2Fnar.2Fgkt1203
  4. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1093.2Fnar.2Fgkt1225
  5. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1093.2Fnar.2Fgkt1245
  6. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0081072
Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.

Posted to the GMOD News on 2013/12/06