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Data Sets, Methods, and Resources: SlGDB



About SLGDB160

SLGDB160 is a BAC-based genome encompassing primary sequence data from Solanum lycopersicum GenBank . 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 SlGDB. To view a different genome version, select from the dropdown above. For more information, visit our Genome Browser Help

Genome Data

Genome Type:BAC
Genome Source: GenBank
Genome Assembly Version:SLGDB160
Total Genome Segments:423
Masking Datasets:

Transcript Alignments


EST- Total cognate alignments:44,144
EST Version:160
cDNA- Total cognate alignments:568
cDNA Version:160
PUT- Total alignments:11,088
PUT Version: 157

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

Gene Models

Total gene annotations:0
Gene Model Version:GenBank
Total yrGATE Community Annotations:0

Protein Alignments

Protein 1: Arabidopsis thaliana (AtPEP) total count:876
Protein 1 Version:AtPEP

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: Generic

Parameters: Default

Probe

tomato10k:Total alignments: 112,528

Alignment Methods

VMatch, Version 1.9

BLAST, Version 2.2.15


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