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Data Sets, Methods, and Resources: ZxGDB



About ZMUPDATE

ZMUPDATE is a BAC-based genome encompassing primary sequence data from Zea mays 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 ZxGDB. 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:ZMUPDATE
Total Genome Segments:35649
Masking Datasets:

Transcript Alignments


EST- Total cognate alignments:3,102,842
EST Version:0
cDNA- Total cognate alignments:101,779
cDNA Version:0
PUT- Total alignments:587,139
PUT Version: 163

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:1,512
Gene Model Version:GenBank
Total yrGATE Community Annotations:205

Protein Alignments

Protein 1: Rice Protein (OsPEP) total count:28,417
Protein 1 Version:OsPEP
Protein 2: Sorghum Protein (SbPEP) total count:124,562
Protein 2 Version:SbPEP

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

Maize58k:Total alignments: 323,134

Alignment Methods

VMatch, Version 1.9

BLAST, Version 2.2.15


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