Genome Data
| Genome Type: | Chromosome |
| Genome Source: | Phytozome 5.0/brachypodium.org |
| Genome Assembly Version: | JGI v1.0 8x assembly |
| Total Genome Segments: | 6 |
| Masking Datasets: | |
Transcript Alignments
| EST- Total cognate alignments: | 125,927 |
| EST Version: | 179 |
| cDNA- Total cognate alignments: | 4 |
| cDNA Version: | 179 |
| PUT- Total alignments: | 25,562 |
| PUT Version: | 175a |
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: | 32,255 | | Gene Model Version: | MIPS/JGI v1.2 | | Total yrGATE Community Annotations: | 0 |
Protein Alignments
| Protein 1: Arabidopsis thaliana (TAIR9) total count: | 13,571 | | Protein 1 Version: | TAIR9 | | Protein 2: Medicago truncatula (Mt3.0) total count: | 10,090 | | 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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