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Data Sets, Methods, and Resources: SbGDB



About SbGDB181

SbGDB181 is a Chromosome-based genome encompassing primary sequence data from Sorghum bicolor Sbi1 . 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 SbGDB. 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: Sbi1
Genome Assembly Version:SbGDB181
Total Genome Segments:10
Masking Datasets:

Transcript Alignments


EST- Total cognate alignments:174,662
EST Version:181
cDNA- Total cognate alignments:203
cDNA Version:181
PUT- Total alignments:31,840
PUT Version: 157

Alignment Methods

GeneSeqer
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:29,448
Gene Model Version:sb1.4
Total yrGATE Community Annotations:26

Protein Alignments

Protein 1: Oryza sativa (OSpep) total count:13,715
Protein 1 Version:OSpep

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

Probe

:Total alignments:

Alignment Methods

VMatch, Version 1.9

BLAST, Version 2.2.15


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