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Data Sets, Methods, and Resources: AtGDB



About AtGDB171

AtGDB171 is a Chromosome-based genome encompassing primary sequence data from Arabidopsis thaliana TAIR 9 . 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 AtGDB. 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: TAIR 9
Genome Assembly Version:AtGDB171
Total Genome Segments:5
Masking Datasets:

Transcript Alignments


EST- Total cognate alignments:1,435,214
EST Version:171
cDNA- Total cognate alignments:82,366
cDNA Version:171
PUT- Total alignments:306,137
PUT Version: 169

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:37,761
Gene Model Version:TAIR9
Total yrGATE Community Annotations:0

Protein Alignments

Protein 1: Rice Protein (OsPEP) total count:5,572
Protein 1 Version:OsPEP

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

ATH1 22k:Total alignments: 251,078

Alignment Methods

VMatch, Version 1.9

BLAST, Version 2.2.15


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