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Data Sets, Methods, and Resources: BdGDB

About BdGDB179

BdGDB179 is a Chromosome-based genome encompassing primary sequence data from Brachypodium distachyon Phytozome 5.0 /brachypodium.org. 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 BdGDB. 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 5.0/brachypodium.org
Genome Assembly Version:JGI v1.0 8x assembly
Total Genome Segments:6
Masking Datasets:

Transcript Alignments

EST- Total cognate alignments:125,927
EST Version:179
cDNA- Total cognate alignments:4
cDNA Version:179
PUT- Total alignments:25,562
PUT Version: 175a

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:32,255
Gene Model Version:MIPS/JGI v1.2
Total yrGATE Community Annotations:0

Protein Alignments

Protein 1: Arabidopsis thaliana (TAIR9) total count:13,571
Protein 1 Version:TAIR9
Protein 2: Medicago truncatula (Mt3.0) total count:10,090
Protein 2 Version:Mt3.0

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: 0

Alignment Methods

VMatch, Version 1.9

BLAST, Version 2.2.15

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