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Data Sets, Methods, and Resources: RcGDB



About RcGDB179

RcGDB179 is a Scaffold-based genome encompassing primary sequence data from Ricinus communis TIGR/JCVI v0.1 . 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 RcGDB. 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: TIGR/JCVI v0.1
Genome Assembly Version:RcGDB179
Total Genome Segments:5441
Masking Datasets:

Transcript Alignments


EST- Total cognate alignments:61,023
EST Version:179
cDNA- Total cognate alignments:123
cDNA Version:179
PUT- Total alignments:16,354
PUT Version: 163a

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:31,221
Gene Model Version:
Total yrGATE Community Annotations:0

Protein Alignments

Protein 1: Arabidopsis thaliana (TAIR9) total count:4,079
Protein 1 Version:TAIR9
Protein 2: Medicago truncatula (Mt3.0) total count:3,977
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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