Medicago truncatula -- MedicCyc

A recent article from Bioinformatics discusses a visual biochemical pathway database -- MedicCyc -- for Medicago truncatula -- "Metabolic pathway reconstruction was used to generate a pathway database for M. truncatula (MedicCyc), which currently features more than 250 pathways with related genes, enzymes and metabolites."

Urbanczyk-Wochniak E, Sumner LW. MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics. 2007 Jun 1;23(11):1418-23. Epub 2007 Mar 7.

Article
PubMed

Illumina BeadChip platform

Illumina Seminar
Keating Room 103 -- Large Meeting room off of Lobby
GATC will be hosting a seminar from Illumina concerning the applications of their "next generation sequencing"platform. The topics being presented are:

• Whole Genome and Candidate Resequencing
• SNP Mutation Discovery
• Digital Gene Expression Profiling
• ChIP by Sequence Tagging
• Small RNA/miRNA Identification and Quantitation

All are welcome to attend, the talk should last about an hour and there will be
time for questions after. Call or email Ryan Sprissler / 520.621.9184 / ryans1@email.arizona.edu

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A recent article describes IlluminaGUI -- a graphical user interface implemented for analyzing microarray data from the Illumina BeadChip platform

Article -- IlluminaGUI: Graphical User Interface for analyzing gene expression data generated on the Illumina platform

Link

CRISPRdb database

The CRISPRdb database is a browsable sequence-database of "clustered regularly interspaced short palindromic repeats" from Archeae and Bacteria.

Each month, the CRISPRFinder program searches several sources for new CRISPRs, and updates the CRISPRdb database. CRISPRFinder can be downloaded and used to search locally generated data as well.


- About
- Link

Browse by
- View the strains taxonomy browser
- View the strains alphabetical browser
- View the strains in database processing order

Allen Brain Atlas

The Neuroscience Gateway, published in association with Nature, focuses on the genetics of the mammalian brain. Its Allen Brain Atlas can be searched by gene names, markers and symbols, anatomic structure or fine structure annotation. It can be browsed by

• Structure -- Cerebellum / Cerebral cortex / Hippocampal region / Hippocampal formation / Hypothalamus / Lateral septal complex / Midbrain / Medulla / Olfactory bulb / Pons / Pallidum / Retrohippocampal region / Striatum-like amygdalar nuclei / Striatum / Striatum dorsal region / Striatum ventral region / Thalamus
• Gene symbol
• Images -- Coronal or Sagittal

Searches return basic information about the gene, plus links to NCBI and other sources. Running your mouse over the Epression Level/Expression Density bar changes the image to show the anatomic area.

Plant genomic/proteomic sources

PlantGDB -- Plant Genome Database. "an NSF-funded project ... to develop plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities."
- About
- Link

MIPS Plants Databases - Munich Center for Protein Sequences set of databases "focuses on the bioinformatics of plant genomes. It developed from the Arabidopsis genome annotation group." Databases include maize, Arabidosis, rice, tomatoes, lotus, and Medicago. Notable for manual annotations.
- About
- Link

iMap -- "Maize Mapping Project is to develop a fully integrated genetic and physical map for maize. To display this integrated map, we have developed iMap. iMap has three main components: a relational database (iMapDB), a map graphic browser (iMap Viewer) and a search utility (iMap Search). iMapDB is populated with current genetic and physical map data, describing relationships among genetic loci, molecular markers and bacterial artificial chromosome (BAC) contigs."
- About
- Link

Other databases -- "DataBases: Web sites for Chromosome Researchers." Scroll down to Plants.