Genome Data
| Genome Type: | Chromosome |
| Genome Source: | TAIR 9 |
| Genome Assembly Version: | AtGDB171 |
| Total Genome Segments: | 5 |
| Masking Datasets: | |
Transcript Alignments
| EST- Total cognate alignments: | 1,435,214 |
| EST Version: | 171 |
| cDNA- Total cognate alignments: | 82,366 |
| cDNA Version: | 171 |
| PUT- Total alignments: | 306,137 |
| PUT Version: | 169 |
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: | 37,761 | | Gene Model Version: | TAIR9 | | Total yrGATE Community Annotations: | 0 |
Protein Alignments
| Protein 1: Rice Protein (OsPEP) total count: | 5,572 | | 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:
Parameters: Default
Probe
| ATH1 22k: | Total alignments: 251,078 |
Alignment Methods
VMatch, Version 1.9
BLAST, Version 2.2.15
|