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Data Sets, Methods, and Resources: PeGDB



About PeGDB179

PeGDB179 is a Scaffold-based genome encompassing primary sequence data from Prunus persica Version1.179 . 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 PeGDB. To view a different genome version, select from the dropdown above. For more information, visit our Genome Browser Help

Genome Data

Genome Type:Scaffold
Genome Source: Version1.179
Genome Assembly Version:PeGDB179
Total Genome Segments:202
Masking Datasets:

Transcript Alignments


EST- Total cognate alignments:114,018
EST Version:179
cDNA- Total cognate alignments:236
cDNA Version:179
PUT- Total alignments:35,875
PUT Version: 171a

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:28,702
Gene Model Version:
Total yrGATE Community Annotations:0

Protein Alignments

Protein 1: Arabidopsis thaliana (TAIR9) total count:3,688
Protein 1 Version:TAIR9
Protein 2: Medicago truncatula (Mt3.0) total count:3,572
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

:Total alignments: 0

Alignment Methods

VMatch, Version 1.9

BLAST, Version 2.2.15


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