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Data Sets, Methods, and Resources: SmGDB



About

is a Scaffold-based genome encompassing primary sequence data from Selaginella moellendorffii Version183/Phytozome v7.0 . 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 SmGDB. 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: Version183/Phytozome v7.0
Genome Assembly Version:SmGDB183
Total Genome Segments:768
Masking Datasets:

Transcript Alignments


EST- Total cognate alignments:147,864
EST Version:183
cDNA- Total cognate alignments:0
cDNA Version:183
PUT- Total alignments:37,083
PUT Version: 165a

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:22,285
Gene Model Version:
Total yrGATE Community Annotations:0

Protein Alignments

Protein 1: Arabidopsis thaliana () total count:2,240
Protein 1 Version:
Protein 2: Medicago truncatula (Mt3.0) total count:1,726
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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