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Data Sets, Methods, and Resources: PtGDB



About PtGDB179

PtGDB179 is a Chromosome-based genome encompassing primary sequence data from Populus trichocarpa Ptr v2.0 /ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v5.0/. 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 PtGDB. 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: Ptr v2.0/ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v5.0/
Genome Assembly Version:Ptr v2.0
Total Genome Segments:20
Masking Datasets:

Transcript Alignments


EST- Total cognate alignments:82,162
EST Version:179
cDNA- Total cognate alignments:4,496
cDNA Version:179
PUT- Total alignments:23,759
PUT Version: 157a

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:45,778
Gene Model Version:Ptr v2.2
Total yrGATE Community Annotations:17

Protein Alignments

Protein 1: Arabidopsis thaliana (TAIR9) total count:6,289
Protein 1 Version:TAIR9
Protein 2: Medicago truncatula (Mt3.0) total count:5,487
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

Affymetrix:Total alignments: 674,330

Alignment Methods

VMatch, Version 1.9

BLAST, Version 2.2.15


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