Part I: Tips and Techniques from curators

Slides:

Advertisements

Similar presentations

Gene Structure Annotation David Swarbreck ASPB Plant Biology, June 29, 2008, Merida.

Advertisements

Making best use of TAIR tools and datasets Philippe Lamesch Donghui Li The Arabidopsis Information Resource contact us:

TAIR: Bringing together data for the global plant biology community Philippe Lamesch Kate Dreher The Arabidopsis Information Resource

GBrowse at TAIR Philippe Lamesch TAIR curator. Seqviewer.

Gene Structure Annotation Philippe Lamesch International Arabidopsis conference July 23, 2008, Montreal.

Part I: Tips and Techniques from curators GBrowse at TAIR David Swarbreck.

Eukaryotic Intron Loss Tobias Mourier & Daniel C. Jeffares.

Introduce GeneSpring GX12 Yun Lian GeneSpring Layout.

NCBI National Center for Biotechnology Information.

1/30 Comparative Genomics. 2/30 Overview of the Talk Comparing Genomes Homologies & Families Sequence Alignments.

First release of HOGENOM, a database of homologous genes from complete genome Equipe Bioinformatique et Génomique Evolutive Laboratoire de Biométrie et.

Selection on codons OEB Degenerate Code.

Sequence-Structure-Function Sequence Structure Function Threading Ab initio BLAST Folding: impossible but for the smallest structures Function prediction.

Defining the Regulatory Potential of Highly Conserved Vertebrate Non-Exonic Elements Rachel Harte BME230.

BioSci 145B lecture 1 page 1 © copyright Bruce Blumberg All rights reserved mRNA frequency and cloning mRNA frequency classes –classic references.

Selection upon codons BIOS E *Aside: shallow trees are strange… And ignore question 7. of assignment…

EVOLUTIONARY AND COMPUTATIONAL GENOMICS Shin-Han Shiu Plant Biology / CMB / EEBB / Genetics / QBMI.

TAIR resources for plant biology research kate dreher curator TAIR/PMN.

The Ensembl Gene set The “Genebuild” 21 April 2008.

TAIR, PMN, SGN and Gramene workshop Focus on comparative genomics and new tools Philippe Lamesch, A. S. Karthikeyan, Aureliano Bombarely Gomez, Pankaj.

Using The Gene Ontology: Gene Product Annotation.

Genome Characterization Assembly/sequencing BIO520 BioinformaticsJim Lund Assigned reading: Ch 9.

Genomes School B&I TCD Bioinformatics May Genome sizes Completed eukaryotic nuclear genomes Type of organismSpeciesGenome size (10 6 base pairs)

EBI is an Outstation of the European Molecular Biology Laboratory. Bert Overduin Daniel Rios Stephen Fitzgerald Edinburgh, 24 & 25 February 2009 Ensembl.

Ontologies, data standards and controlled vocabularies.

Eukaryotic Genomes: From Parasites to Primates (part 2 of 2) Monday, November 3, 2003 Introduction to Bioinformatics ME: J. Pevsner

Comparative genomics and proteomics in Ensembl Sep 2006.

An Introduction to Ensembl Presented By Hilary O. Pavlidis.

1/29 Comparative Genomics. 2/29 Overview of the Talk Comparing Genomes Homologies & Families Sequence Alignments.

EBI is an Outstation of the European Molecular Biology Laboratory. GOA: Looking after GO annotations Emily Dimmer Gene Ontology Annotation (GOA) Database.

Browsing the Genome Using Genome Browsers to Visualize and Mine Data.

whole-genome duplications and large segmental duplications… …seem to be a common feature in eukaryotic genome evolution …play a crucial role in the evolution.

Comparative genomics Haixu Tang School of Informatics.

Evolution of Animal Cytochromes P450 from Sponges to Mammals David R. Nelson University of Tennessee Health Sciences Center Memphis.

Gene models and proteomes for Saccharomyces cerevisiae (Sc), Schizosaccharomyces pombe (Sp), Arabidopsis thaliana (At), Oryza sativa (Os), Drosophila melanogaster.

Lecture/Lab 7.31

Sequence-Structure-Function Sequence Structure Function Threading Ab initio BLAST Folding: impossible but for the smallest structures Function prediction.

What’s new in GO?. Priorities Annotation outreach Reference genomes User advocacy Ontology development Software.

Tools For Vertebrate Gene Naming

B. subtilis as query species

Annotating with GO: an overview

Genetics and Evolutionary Biology

Some of the organisms that are used as highly informative models to study gene action and development. (a) Escherichia coli is a common bacterium; (b)

The Refgene Database.

Genome Projects Maps Human Genome Mapping Human Genome Sequencing

TAIR, PMN, SGN and Gramene workshop

Fejlődésbiológiai technikák, modellek

Introduction to Bioinformatics II

Chromosome Number in Species

Ensembl Genome Repository.

Methods in developmental biology

Mutation Altering the miR-184 Seed Region Causes Familial Keratoconus with Cataract Anne E. Hughes, Declan T. Bradley, Malcolm Campbell, Judith Lechner,

miR-122, a paradigm for the role of microRNAs in the liver

Mutations in ZDHHC9, Which Encodes a Palmitoyltransferase of NRAS and HRAS, Cause X-Linked Mental Retardation Associated with a Marfanoid Habitus F.

by , Christine G. Elsik, Ross L. Tellam, and Kim C. Worley

RSPO4 Is the Major Gene in Autosomal-Recessive Anonychia and Mutations Cluster in the Furin-Like Cysteine-Rich Domains of the Wnt Signaling Ligand R-spondin.

Allelic Heterogeneity in the COH1 Gene Explains Clinical Variabilityin Cohen Syndrome Hans Christian Hennies, Anita Rauch, Wenke Seifert, Christian Schumi,

(A) Six missense mutations in six essential genes that are not in annotated functional domains. (A) Six missense mutations in six essential genes that.

Figure 2 DNA sequence analysis of VPS37A

Mutations in ZDHHC9, Which Encodes a Palmitoyltransferase of NRAS and HRAS, Cause X-Linked Mental Retardation Associated with a Marfanoid Habitus F.

Computational genomics

VPS35 Mutations in Parkinson Disease

Satoshi Suzuki, Mary L. Marazita, Margaret E

Part II SeqViewer AraCyc Help

Homologs in 38 fully sequenced eukaryotic genomes to 534 assigned S

How to search NCBI.

Missense Mutation in Pseudouridine Synthase 1 (PUS1) Causes Mitochondrial Myopathy and Sideroblastic Anemia (MLASA) Yelena Bykhovskaya, Kari Casas, Emebet.

Alignment of Wt1 genomic regions reveals a highly conserved element upstream of zebrafish wt1a. Alignment of Wt1 genomic regions reveals a highly conserved.

Rtt101 and Mms1 in budding yeast form a CUL4DDB1‐like ubiquitin ligase that promotes replication through damaged DNA Mms1 belongs to the DDB1 family of.

Angioid Streaks in Pseudoxanthoma Elasticum: Role of the p

Presentation transcript:

Part I: Tips and Techniques from curators GBrowse at TAIR David Swarbreck

TAIR9 Genome Release

TAIR9 - Sources of data New cDNA/EST data, x-species alignments Updates from proteome data Baerenfaller et al., 2008 and Castellana et al., 2008 Analysis of pseudopipe annotations Mark Gerstein’s lab Analysis of alternative gene predicitions Gnomon - Alexandre Souvorov Eugene - Sébastien Aubourg Aceview - Jean Thierry-Mieg

TAIR9 Genome release 282 new loci, 739 new gene models 1254 modified models, 774 CDS updates 1144 modified exons, 1056 new exons Contains: 33518 genes total, 39640 gene models 27,379 protein coding genes 4827 pseudogenes/TE genes 1312 ncRNAs

Genome Browsers at TAIR Two options (Seqviewer & GBrowse)

Seqviewer

Seqviewer

GBrowse Header Main Browser Window Track Menu

GBrowse - Header Configure Vista plot & fasta download Search by: Feature Name AT1G01040 AY438620 Position Chr2:100500..102500

Track menu

Proteomics Data Baerenfaller 2008 Castellana et al. 2008

Reposition tracks

VISTA plot Gbrowse track Dubchak et al

Orthologs and Gene Families INSECTS Aedes aegypti (Yellow fever mosquito) Anopheles gambiae (Malaria mosquito) Apis mellifera (Western honeybee) Drosophila melanogster (Fly) Drosophila pseudoobscura (Fly) MAMMALS Bos taurus (Cow) Canis familiaris (Dog) Homo sapiens (human) Mus Musculus (mouse) Gallus gallus (Chicken) Macaca mulatta (Rhesus Macaque) Monodelphis domestica (Opossum) Pan troglodytes (Chimpanzee) Rattus norvegicus (Rat) YEAST Candida gablata (Haploid yeast) Cryptococcus neoformans (Yeast-like fungus) Debaryomyces hansenii (Yeast) Kluyveromyces lactis (Yeast) Yarrowia lipolytica (yeast) Schizosaccharomyces pombe (Fission yeast) Saccharomyces cerevisiae (Budding yeast) FISH Takifugu rubripes (Pufferfish/Fugu) Tetraodon nigroviridis (Pufferfish/Green-spotted) Gasterosteus aculeatus (Stickleback) Danio rerio (Zebrafish) NEMATODES Caenorhabditis elegans (Nematode) Caenorhabditis briggsae (Nematode) Caenorhabditis remanei (Nematode) PLANTS Oryza sative (rice) OTHER Xenopus tropicalis (Frog) Ciona intestinalis (Sea squirt) Entamoeba histolytica (Amoebozoa) Dictyostelium discoideum (Slime mold)

Orthologs and Gene Families

Promoter Elements

Tracks updated regularly

Gene Confidence Rank Attributes confidence scores to all exons and gene models based on different types of experimental and computational evidence

Assigning A Confidence Rank

Full support No support

How can I upload my own annotations to GBrowse ? http://www.arabidopsis.org/cgi-bin/gbrowse/arabidopsis/?help=annotation

How can I download a marked up FASTA file of a particular region?

Decorated Fasta file

Decorated Fasta file

Coming Soon Synteny viewer