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Data Sets, Methods, and Resources: CpGDB



About CpGDB181

CpGDB181 is a Scaffold-based genome encompassing primary sequence data from Carica papaya Version1.181 . 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 CpGDB. 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: Version1.181
Genome Assembly Version:CpGDB181
Total Genome Segments:5901
Masking Datasets:

Transcript Alignments


EST- Total cognate alignments:62,535
EST Version:181
cDNA- Total cognate alignments:120
cDNA Version:179
PUT- Total alignments:19,114
PUT Version: 167a

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:27,792
Gene Model Version:
Total yrGATE Community Annotations:0

Protein Alignments

Protein 1: Arabidopsis thaliana (TAIR9) total count:3,550
Protein 1 Version:TAIR9
Protein 2: Medicago truncatula (Mt3.0) total count:2,793
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:

Alignment Methods

VMatch, Version 1.9

BLAST, Version 2.2.15


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