Physcomitrella patens scaffold sequences
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->
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Ordered series of contigs with or without gaps.
(Total: 2106)
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Genome / Gene Models
The genome assembly displayed at PpGDB is version
Phypa1_1;
gene models are from
Phypa1_1.
More about the genome...
Physcomitrella patens genome at PpGDB
| Type |
Count |
Total Length (bp) |
Gene Models |
| Phase 3 | 0 | | 0 |
| Phase 2 | 0 | | 0 |
| Phase 1 | 2,106 | 479,985,347 | 35,938 |
| Total: |
|---|
| 2,106 | 479,985,347 | 35,938 |
Alignments to Genome
PpGDB displays high quality spliced alignments for EST, cDNA, PUT, Os-PEP, Probe;
DNA alignments include [none].
Search / Download
You can search or download any splice-aligned sequences, gene models, or genomic sequence from PpGDB. The entire PpGDB dataset can also be downloaded.
More about search / download...
Search / Download - Description
| Resource |
Description |
| Search by ID / Keyword |
Search for any PpGDBgene or aligned sequence by ID or keyword, and download complete sequence or flanking 5' or 3' regions, exons, or introns (FASTA format).
|
| Download Region Data |
For any specified genomic region, download genomic DNA (FASTA format), all aligned/computed transcripts or proteins (FASTA format), or all genome annotations (GenBank, GFF3 or EMBL format).
|
| Download All |
Download bzip2 files and MySQL tables representing complete PpGDB dataset |
View the latest Physcomitrella patens sequence count at PlantGDB.
Tools
Sequence analysis tools accessed from the
Genome Context View menu use the current genomic region as input. Or, to access the same tools without a genomic context, use PpGDB left menubar Tools links.
More about tools...
Online Analytical Tools - Description
| Name |
Description |
Source/Version |
| BLAST |
Use BLASTn, BLASTp, tBLASTn and tBLASTx to match a query sequence to PpGDB sequences.
BLAST-able datasets include Physcomitrella patens genomic DNA, splice-aligned transcripts and proteins, gene models, and other aligned sequences. |
NCBI Blastall 2.2.18 |
| GeneSeqer |
Spliced alignment of user-specified transcript datasets to genomic DNA from any region in PpGDB. User can specify splice site model and stringency level. |
Brendel Group (Oct 2008) |
| GenomeThreader |
Spliced alignment of user-specified protein datasets to genomic DNA from any region in PpGDB. User can specify splice site model and stringency level. |
GenomeThreader Home Page |
Community Annotation
Help annotate the
Physcomitrella patens genome using our yrGATE gene structure annotation tool (
see Overview), aided by
GAEVAL tables that flag problematic gene models.
Video demo: QuickTime
Flash
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Custom Track Display
Distributed Annotation Service (DAS) (
see Overview) is available for displaying remotely served genome alignments at PpGDB, as well as for displaying selected PpGDB tracks on a different genome browser (e.g. Ensembl, GBrowse).
How to use DAS...
To add a DAS track to PpGDB using our DAS client, first select desired genome coordinates above and click "Go", then select menu item "Configure -> Add Track" and paste in the appropriate DAS URL.
To view PpGDB tracks in another genome browser (e.g. Ensembl, Gbrowse) using our DAS server, first find the appropriate xDAS Server URL on our DAS overview page, then follow instructions on the remote browser website for adding the remote track. NOTE: DAS service available for certain tracks only.
For more details, refer to DAS section in our Genome Browser help pages.
Additional custom track display features are under development.
Annotated Protein Alignments
Support
Genome browser video demo: QuickTime
Flash
For help pages and tutorials focusing on genome browser features and gene annotation, see side bar.