annotation and visualization doreen ware. project challenges rapidly growing sequence data full...
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Annotation and Visualization
Doreen Ware
Project Challenges
•Rapidly growing sequence data
•Full annotation of all clones
•New high-performance computing cluster
•2,000 nodes
•Scheduling system (SunGrid Engine)
•NFS issues
•EnsEMBL Code Integration
Milestones• www.maizesequence.org released
• Customized entry points of the Ensembl browser for the maize community.
• Adapted modules to the new compute cluster Blue Helix and automated gene predictions, MDR analysis, repeat masker
• Alignments of cereal sequence using Gramene Biopipe (needs to be automated)
• Transitioned from annotating Finished BACs to all BACs as they become available
• Blast Server
• FTP site
• DAS server (displaying Twinscan annotations)
Index Page
Maizesequence.org RSS BAC Notification
• Users can be notified of sequence and annotation updates to a particular region of interest on the FPC map via a RSS (Really Simple Syndication) notification system.
• Data is delivered as XML to the user’s favorite feed reader or is parsed in RSS enabled browsers.
• The URL for any given query is persistent and dynamically retrieves database updates in the user-specified region.
…
www.maizesequence.org/Zea_mays/notification
Maizesequence.org FTP and Blast DB
Ensembl BAC DB
Weekly
Bulk Genome Dump
Maize FTP
BACsBAC Contigs
Ab initio predictionsAb initio translations
Maize Blast
BAC ContigsAb initio predictionsAb initio translations
• BACs, BAC Contigs, FgenesH predictions (TE and non-TE classes), and FgenesH translations are dumped on a weekly basis.
• Sequence dumps are posted to the FTP site. (ftp.maizesequence.org)
• Sequence dumps are also used to update the blast databases. (www.maizesequence.org/Multi/blastview)
MapView
CytoView
ContigView
GeneView
GeneView
ExportView
ExportView
ExportView
Maize Databases and Annotation Pipeline
Classification of Gene Models
• Ab initio gene prediction on non-masked contigs with FGENESH using Monocot parameters.
• Classified gene models by BLASTP to Genbank NRAA.
• TE = Alignment to transposable elements (TE), as specified within curated database.
• NH = No detectable homology.
• WH = Significant alignment to non-TE.
• Corrupted_translation = Ensembl translation inconsistent with FGENESH.
Gene Model Class Minimum Maximum Average Median
Standard Deviation
TE size (bases) 51 23,913 2,739 2,402 1,916
WH size (bases) 73 25,816 2,465 1,829 2,146
NH size (bases) 3 19,465 975 645 944
Corrupted_translation (bases)
8 25,869 2,251 1,845 1,813
10,352 Annotated BACs (309,845 Gene Models)
TENHWHCorrupted_translation
TE, 198580, 64%
NH, 51805, 17%
WH, 45055, 14%
Corrupted_Translation, 14405, 5%
Data generated as of September 2007
Nucleotide Coverage of Mathematically-Defined Repats in 10,352 Annotated BACs
(130,978 Contigs)
MDR Type*Total Nucleotides
Nucleotide Coverage
2 copies 1,325,811,407 79.11%
10 copies 937,789,153 55.96%
100 copies
602,350,024 35.94%
1000 copies
218,650,689 13.05%
*Mathematically defined repeats indicate regions of repetitive DNA. The frequency of each constituent 20-mer along the BAC sequence was determined within the raw reads of the maize whole genome shotgun sequence (DOE Joint Genome Institute). “MDR type 2 copies” indicates regions over which 20-mers occurred two or more times. Thus, “MDR type 10 copies”, “MDR type 100 copies”, and “MDR type 1000 copies” indicate; respectively, regions over which 20-mers occurred, ten or more times, one hundred or more times, and one thousand or more times. The most repetitive regions correspond to regions in the MDR type 1000 copies. The least repetitive regions correspond to areas in the MDR type 2 copies.
Data generated as of September 2007
Nucleotide Coverage of Repeats in 10,352 Annotated BACs (130,978
Contigs)
Repeat Type*Total Nucleotides
Nucleotide Coverage
MIPS/REcat Class I Retroelements 1,503,929,793 75.66%
MIPS/REcat Class II/III Transposable Elements
36,620,646 1.84%
MIPS/Recat Other 16,048,937 0.81%
All Repeats 1,553,118,769 78.13%
*Repetitive sequences were annotated and masked using RepeatMasker and the MIPS-Redat library.
Data generated as of September 2007
Outreach and Collaborations
•MaizeGDB•EBI EnsEMBL•Gramene•Maize Array Working Group
•Maize Optical Map
•Transposon Annotation
•TWINSCAN•Vmatch•Student Annotation (Howard Hughes)
Objectives for Year 3
• Whole Genome Alignments for rice, maize and arabidopsis
• Evidence based gene builds Gramene modified Ensembl pipeline and FGENESH++ in combiner mode BioMart for complex query generation
• Whole Genome Alignments for rice, maize and arabidopsis
• SyntenyView based on whole genome alignment• Transition from Gramene Biopipe -> Ensembl
Exonerate pipeline to automate sequence alignments• Annotation of non-coding RNA using tRNAScan and
microRNA • Gene Ontology using dbxref pipeline• Incorporation in Gramene Compara builds; GeneTree
view• MySQL Database dumps• Tutorials for website using Camptasia• Submit paper on MDR analysis
Shiran Pasternak, Apurva Narechania, Linda McMahan, Joshua Stein