Genome Data
| Genome Type: | Chromosome |
| Genome Source: | Kazuza.org/Lj1.0 |
| Genome Assembly Version: | LjGDB171 |
| Total Genome Segments: | 7 |
| Masking Datasets: | |
Transcript Alignments
| EST- Total cognate alignments: | 130,579 |
| EST Version: | |
| cDNA- Total cognate alignments: | 300 |
| cDNA Version: | |
| PUT- Total alignments: | 40,638 |
| PUT Version: | 171 |
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: | 22,650 | | Gene Model Version: | Lj1.0 | | Total yrGATE Community Annotations: | 2 |
Protein Alignments
| Protein 1: Arabidopsis thaliana (AtPEP) total count: | 7,328 | | Protein 1 Version: | AtPEP |
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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