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Data Sets, Methods, and Resources: HvGDB



About HVGDB157

HVGDB157 is a BAC-based genome encompassing primary sequence data from Hordeum vulgare GenBank . 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 HvGDB. To view a different genome version, select from the dropdown above. For more information, visit our Genome Browser Help

Genome Data

Genome Type:BAC
Genome Source: GenBank
Genome Assembly Version:HVGDB157
Total Genome Segments:59
Masking Datasets:

Transcript Alignments


EST- Total cognate alignments:9,935
EST Version:157
cDNA- Total cognate alignments:166
cDNA Version:157
PUT- Total alignments:1,309
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: Maize
Parameters: -m 999999999 -x 30 -y 45 -z 60
m - maxnest
x - wordsize
y - minqHSP
z - minqHSPc

Gene Models

Total gene annotations:328
Gene Model Version:GenBank
Total yrGATE Community Annotations:1

Protein Alignments

Protein 1: Rice Protein (OsPEP) total count:152
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: Maize

Parameters: Default

Probe

Barley1:Total alignments: 251,437

Alignment Methods

VMatch, Version 1.9

BLAST, Version 2.2.15


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