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Data Sets, Methods, and Resources: GxGDB



About GMGDB163

GMGDB163 is a Scaffold-based genome encompassing primary sequence data from Glycine max Glyma0 /Glyma0/Gbk. 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 GxGDB. 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: Glyma0/Glyma0/Gbk
Genome Assembly Version:GMGDB163
Total Genome Segments:3423
Masking Datasets:

Transcript Alignments


EST- Total cognate alignments:626,932
EST Version:163
cDNA- Total cognate alignments:2,980
cDNA Version:163
PUT- Total alignments:149,932
PUT Version: 161

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: Medicago
Parameters: -m 999999999 -x 30 -y 45 -z 60
m - maxnest
x - wordsize
y - minqHSP
z - minqHSPc

Gene Models

Total gene annotations:62,442
Gene Model Version:Glyma0.1b
Total yrGATE Community Annotations:0

Protein Alignments

Protein 1: Arabidopsis thaliana (AtPEP) total count:14,945
Protein 1 Version:AtPEP
Protein 2: Medicago truncatula (MtPEP) total count:43,302
Protein 2 Version:MtPEP

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: Medicago

Parameters: Default

Probe

Soybean:Total alignments: 671,762

Alignment Methods

VMatch, Version 1.9

BLAST, Version 2.2.15


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