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Data Sets, Methods, and Resources: LjGDB



About LjGDB171

LjGDB171 is a Chromosome-based genome encompassing primary sequence data from Lotus japonicus Kazuza.org /Lj1.0. The mapping of cDNA and EST sequences onto the genome as well as interpretations of the overall data are based on our own spliced alignment results. The information below summarizes the data sets and methods used for the selected version of LjGDB. To view a different genome version, select from the dropdown above. For more information, visit our Genome Browser Help

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

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

:Total alignments:

Alignment Methods

VMatch, Version 1.9

BLAST, Version 2.2.15


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