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Data Sets, Methods, and Resources: OsGDB

About OsGDB187

OsGDB187 is a Chromosome-based genome encompassing primary sequence data from Oryza sativa (ssp. japonica) Phytozome 8.0 /MSU Rice Genome Project. The mapping of cDNA and EST sequences onto the genome as well as interpretations of the overall data are based on our own spliced alignment results. The information below summarizes the data sets and methods used for the selected version of OsGDB. To view a different genome version, select from the dropdown above. For more information, visit our Genome Browser Help

Genome Data

Genome Type:Chromosome
Genome Source: Phytozome 8.0/MSU Rice Genome Project
Genome Assembly Version:MSU Release 7
Total Genome Segments:
Masking Datasets:

Transcript Alignments

EST- Total cognate alignments:
EST Version:GenBank 187
cDNA- Total cognate alignments:
cDNA Version:GenBank 187
PUT- Total alignments:
PUT Version: PlantGDB 163a

Alignment Methods

GeneSeqer is a gene identification tool based on spliced alignment or "spliced threading" of cDNAs/ESTs into a genomic DNA sequence template.
Splicing Model:
Parameters: -m 999999999 -x 30 -y 45 -z 60
m - maxnest
x - wordsize
y - minqHSP
z - minqHSPc

Gene Models

Total gene annotations:
Gene Model Version:MSU Release 7
Total yrGATE Community Annotations:0

Protein Alignments

Protein 1: Arabidopsis thaliana () total count:
Protein 1 Version:
Protein 2: Sorghum bicolor () total count:
Protein 2 Version:

Alignment Methods

GenomeThreader, Version 1.0.8

GenomeThreader is a gene identification tool based on spliced alignment or "spliced threading" of cDNAs/ESTs or proteins into a genomic DNA sequence template
Splicing Model:

Parameters: Default


:Total alignments:

Alignment Methods

VMatch, Version 1.9

BLAST, Version 2.2.15

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