Genome Data
Transcript Alignments
| EST- Total cognate alignments: | 82,162 |
| EST Version: | 179 |
| cDNA- Total cognate alignments: | 4,496 |
| cDNA Version: | 179 |
| PUT- Total alignments: | 23,759 |
| PUT Version: | 157a |
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
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Gene Models
| Total gene annotations: | 45,778 | | Gene Model Version: | Ptr v2.2 | | Total yrGATE Community Annotations: | 17 |
Protein Alignments
| Protein 1: Arabidopsis thaliana (TAIR9) total count: | 6,289 | | Protein 1 Version: | TAIR9 | | Protein 2: Medicago truncatula (Mt3.0) total count: | 5,487 | | Protein 2 Version: | Mt3.0 |
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: | Total alignments: 674,330 |
Alignment Methods
VMatch, Version 1.9
BLAST, Version 2.2.15
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