Gramene

Release Notes July 2005

New Genomes Data

Mapping to the Oryza sativa (japonica) genome of flanking sequences for the Oryza sativa SNPs from NCBI's dbSNP build 34.

Alignments were performed using the Ensembl Variation mapping pipeline which in turn uses the SSAHA algorithm.
Of the ~3,900,000 rice SNPs in dbSNP, ~2,900,000 were mapped to the genome; ~2,700,000 to a unique location.

Mapping to the Oryza sativa (japonica) genome of microarray target (concensus) sequences from the following chips;

Wheat Affymetrix 61K GeneChip (targets Triticum aestivum, T. monococcum, T. turgidum and Aegilops tauschii sequences), 61115 sequences, of which 21616 (35.35%) mapped.
Rice Affymetrix 57K GeneChip (targets Oryza Sativa sequences). 57194 sequences, of which 47729 (83.45%) mapped.
Maize Affymetrix 18K GeneChip (targets Zea mays sequences), 17555 sequences, of which 10132 (57.72%) mapped.

Mapping to the Oryza sativa (japonica) genome of microarray oligonucleotide reporter sequences from the Rice NSF 20K chip, 20230 sequences of which 18884 (93.3%) mapped. Alignments in the UTR regions of the TIGR gene models are classed as unmapped.

Mapping to the Oryza sativa (japonica) genome of rice MPSS (Massively Parallel Signature Sequencing) oligo sequences. Data supplied by Blake Meyers at University of Delaware. 93301 sequences, of which 92735 (99.4%) mapped. Alignments that cross an exon boundary, or map to organelles, are classed as unmapped.

Mapping to the Oryza sativa (japonica) genome of partial genome assemblies (GSS clusters) for Zea mays (maize). Data supplied by Iowa State University. 214471 sequences, of which 45146 (21.05%) mapped.

Updated mapping of NCBI dbEST sequences for Saccharum (sugarcane). 231225 sequences, of which 134242 (58.06%) mapped.

New Genomes Features

Introduction of GrameneMart: www.gramene.org/Multi/martview

Easy and interactive access to bulk data downloads.
Retrieval of sequences and genome annotations using a variety of filters to constrain retrieved results.
Filters include such things as genomic location and the presence or absence of specific annotations.
Data can be returned in a variety of formats, inluding HTML, text, FASTA, and even Microsoft Excel.
GrameneMart is the Gramene implementation of BioMart.

SnpView

New page for the display of a given SNP.

TransView, ProtView

Addition of information for SNPs that map in the location of the gene,
Options to add SNP markup to the cDNA/peptide sequences,
Table of SNPs and their consequence to the protein,
E.g. LOC_Os01g31460

GeneSnpView

New page for the graphical representation of SNP info in the context of a gene.

ContigView

Addition of an 'Array' menu, used to classify tracks that are derive from array technologies (e.g. microarray chips and MPSS bead arrays). The track names indicate the species, type of sequence, and the array to which they refer. Sequence types include 'Oligo', referring to the reporter (e.g. oligonucleotide) sequences that form the array, and 'Target', to refer to the concensus/exemplar sequences that are identified by the array.
New tracks under the 'Array' menu include;