Genome Data
| Genome Type: | Scaffold |
| Genome Source: | Version1.179 |
| Genome Assembly Version: | PeGDB179 |
| Total Genome Segments: | 202 |
| Masking Datasets: | |
Transcript Alignments
| EST- Total cognate alignments: | 114,018 |
| EST Version: | 179 |
| cDNA- Total cognate alignments: | 236 |
| cDNA Version: | 179 |
| PUT- Total alignments: | 35,875 |
| 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
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Gene Models
| Total gene annotations: | 28,702 | | Gene Model Version: | | | Total yrGATE Community Annotations: | 0 |
Protein Alignments
| Protein 1: Arabidopsis thaliana (TAIR9) total count: | 3,688 | | Protein 1 Version: | TAIR9 | | Protein 2: Medicago truncatula (Mt3.0) total count: | 3,572 | | 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
Alignment Methods
VMatch, Version 1.9
BLAST, Version 2.2.15
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