Genome Data
| Genome Type: | Scaffold |
| Genome Source: | Version1.183 |
| Genome Assembly Version: | Phypa1.1 |
| Total Genome Segments: | 2106 |
| Masking Datasets: | |
Transcript Alignments
| EST- Total cognate alignments: | 379,449 |
| EST Version: | 183 |
| cDNA- Total cognate alignments: | 503 |
| cDNA Version: | 183 |
| PUT- Total alignments: | 42,215 |
| PUT Version: | 169a |
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: | 38,354 | | Gene Model Version: | Phypa1.6 | | Total yrGATE Community Annotations: | 4 |
Protein Alignments
| Protein 1: Arabidopsis thaliana (TAIR9) total count: | 3,937 | | Protein 1 Version: | TAIR9 | | Protein 2: Oryza sativa (JGI v6.0 Osativa_120) total count: | 4,924 | | Protein 2 Version: | JGI v6.0 Osativa_120 |
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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