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
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
Probe
| Affymetrix Maize Genome Array, 18K: | Total alignments: 323,134 |
Alignment Methods
VMatch, Version 1.9
BLAST, Version 2.2.15
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