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Data Sets, Methods, and Resources: PtGDB



About

is a Scaffold-based genome encompassing primary sequence data from Solanum tuberosum PGSC . 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 StGDB. 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: PGSC
Genome Assembly Version:v3_2.1.10
Total Genome Segments:
Masking Datasets:

Transcript Alignments


EST- Total cognate alignments:
EST Version:GenBank 187
cDNA- Total cognate alignments:
cDNA Version:GenBank 187
PUT- Total alignments:
PUT Version: GenBank 187

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:
Gene Model Version:v3.4
Total yrGATE Community Annotations:0

Protein Alignments

Protein 1: Arabidopsis thaliana () total count:
Protein 1 Version:
Protein 2: Medicago truncatula () total count:
Protein 2 Version:

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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