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Data Sets, Methods, and Resources: PpGDB


is a Scaffold-based genome encompassing primary sequence data from Physcomitrella patens Version1.183 . 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 PpGDB. 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: Version1.183
Genome Assembly Version:Phypa1.1
Total Genome Segments:2106
Masking Datasets:

Transcript Alignments

EST- Total cognate alignments:379,449
EST Version:183
cDNA- Total cognate alignments:503
cDNA Version:183
PUT- Total alignments:42,215
PUT Version: 169a

Alignment Methods

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:38,354
Gene Model Version:Phypa1.6
Total yrGATE Community Annotations:4

Protein Alignments

Protein 1: Arabidopsis thaliana (TAIR9) total count:3,937
Protein 1 Version:TAIR9
Protein 2: Oryza sativa (JGI v6.0 Osativa_120) total count:4,924
Protein 2 Version:JGI v6.0 Osativa_120

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


:Total alignments:

Alignment Methods

VMatch, Version 1.9

BLAST, Version 2.2.15

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