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Data Sets, Methods, and Resources: ZmGDB

About ZmGDB181

ZmGDB181 is a Chromosome-based genome encompassing primary sequence data from Zea mays maizesequence.org RefGen_v2 /AGI. 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 ZmGDB. 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: maizesequence.org RefGen_v2/AGI
Genome Assembly Version:ZmGDB181
Total Genome Segments:11
Masking Datasets:Vector + Bacterial + maizesequence.org ZmRepeats (MIPS+MTEC+LTR)

Transcript Alignments

EST- Total cognate alignments:1,448,986
EST Version:181
cDNA- Total cognate alignments:103,793
cDNA Version:181
PUT- Total alignments:148,111
PUT Version: 171a

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:136,522
Gene Model Version:
Total yrGATE Community Annotations:207

Protein Alignments

Protein 1: Oryza sativa (JGI v6.0 Osativa_120) total count:28,814
Protein 1 Version:JGI v6.0 Osativa_120
Protein 2: Sorghum bicolor (JGI v6.0 Sbicolor_79) total count:0
Protein 2 Version:JGI v6.0 Sbicolor_79

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


Affymetrix Maize Genome Array, 18K:Total alignments: 323,134

Alignment Methods

VMatch, Version 1.9

BLAST, Version 2.2.15

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