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ZFIN
Genome Resources WorkshopGenes Genome Sequence Map
Homology Expression
Lynn Schriml: NCBI, Judy Sprague: ZFIN, Kerstin Jekosch: Sanger Institute
Tutorial:
www.ncbi.nlm.nih.gov/genome/guide/zebrafish/Workshop2004
www.ncbi.nlm.nih.gov/genome/guide/zebrafish
http://zfin.org
www.sanger.ac.uk/Projects/D_rerio
Questions and Answers... a guide to genome resources
1. Where do I start ?
2. How do I find my gene ?
3. How do I find gene-related data ?
4. Where can I ask questions or submit suggestions ?
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NCBI includes data from:
• external resourcesmodel organism databases, genome projects, PubMed and GenBank submissions, and datasets provided by the research community
• internal computation
• ongoing curation
1. Where do I start ? www.ncbi.nlm.nih.govWhat kind of data is available ?
NCBI Home Page
• follow the “How to reach us” link to submit questions or submissions
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1. Where do I start ? www.ncbi.nlm.nih.govNCBI Home Page
• navigate to NCBI databases, resources and tools from links provided on NCBI’s home page
• from NCBI’s home page you can submit a query against any of the databases in the pulldown menu
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• begin searches from Entrez Home Page, the Genome Biology Page, or Taxonomy Page
1. Where do I start ? www.ncbi.nlm.nih.govNCBI Home Page
• navigate by links provided on the NCBI home page
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www.ncbi.nlm.nih.govNCBI Home Page1. Where do I start ?
• find out what is new at NCBI from the Highlights on the NCBI home page or from the NCBI newsletter
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• the Genome Biology page provides links to organism specific resource pages
1. Where do I start ? www.ncbi.nlm.nih.gov
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1. Where do I start ? www.ncbi.nlm.nih.gov/Entrez•navigate to individual databases by clicking on database name or icon
• NCBI pre-computes related records between each Entrez database
• From the Entrez home page you can query all Entrez databases by a single text query
•Text queries can include the Boolean terms AND, OR, NOT
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1. Where do I start ? www.ncbi.nlm.nih.gov/Database/datamodel
• The NCBI Entrez integrated search and retrieval system provides pre-computed links between records in disparate databases.
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1. Where do I start ? www.ncbi.nlm.nih.gov/Entrez• view results and link to databases by clicking on the database name or icon
• see examples of records in gene-related resources
•see the summary results of the Entrez global query for the number of records in each Entrez database that matched the text query
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1. Where do I start ? www.ncbi.nlm.nih.gov/genome/guide/zebrafish
• submit a text search in the top search box
• the Zebrafish Genome Resources page includes links to NCBI and Community resources
• click on provided Entrez queries to view the latest papers in PubMed, mRNAs in GenBank, or the complete set of ZGC clones in GenBank
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zgc.nci.nih.gov
1. Where do I start ? www.ncbi.nlm.nih.gov/genome/guide/zebrafish
• The ZGC home page provides inks to order clones and information on full-length clones and ZGC libraries
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1. Where do I start ? www.ncbi.nlm.nih.gov/Taxonomy
•navigate to Zebrafish BLAST, Map Viewer, Trace Archive
• view taxonomic lineage of over 150,000 organisms in sequence databases
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1. Where do I start ? www.sanger.ac.uk/Projects/D_rerio
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clone mapping and sequencingwithmanual annotation in Vega
links to
• mapping project incl. FPC database
• Vega database with
finished/annotated clones
• BLAST server for (un-)finished clone
sequences
• clone status information
1. Where do I start ? www.sanger.ac.uk/Projects/D_rerio
whole genome shotgun assembly integrated with physical mapwithautomated annotation in EnsEMBL
links to
• pre-EnsEMBL database incl.
BLAST/SSAHA server
• EnsEMBL database incl.
BLAST/SSAHA server
• download assemblies
• assembly information
• mapsearch database
• trace repository
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zfin.org
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1. Where do I start ?
Zebrafish Model Organism DatabaseZFIN
Gene Products Gene Expression
Mutant Phenotypes
Sequence InformationMapping Data
Orthology
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1. Where do I start ?
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1. Where do I start ?
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at ZFIN, NCBI and the Sanger Institute
2. How do I find my gene ?
Gene xyz
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2. How do I find my gene ?
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2. How do I find my gene ?
Genomic ContextMapping Panels
Whole Genome Sequence
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2. How do I find my gene ?
• by text search: in Entrez Gene
• by sequence: find related sequences via BLAST
searches or by examining pre-computed sequence comparisons in HomoloGene or BLink (pre-computed protein comparisons)
(find links to BLink results on Entrez protein pages)
• by map position:
query Entrez Gene by map positionorquery map data in Map Viewer
Entrez Gene: www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
BLAST home page: www.ncbi.nlm.nih.gov/BLAST/
HomoloGene: www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene
Map Viewer home page: www.ncbi.nlm.nih.gov/mapview/
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2. How do I find my gene ? www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
• search Entrez Gene by text to find known (named) and unknown genes. Entrez Gene includes records based on uncharacterized cDNAs. These records may represent the gene you are looking for.
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2. How do I find my gene ? www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
• query Entrez Gene by gene attribute : identifier, name, symbol, accession, publication (PubMed ID), GO terms, LG or chromosome
• view results of text query, view detailed results by clicking on the gene symbol
• follow link to Gene Search for additional search options
• Subscribe to resource mailing lists by following Subscriptions link
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2. How do I find my gene ?
• Take advantage of the higher level of annotation available in other genome where your gene of interest has been indentified.
• Beginning with a text search on the gene symbol, choose the Entrez Gene record for a homolog and then look at pre-computed related information.
• Pre-computed nucleotide comparisons in HomoloGene or pre-computed protein comparisons in BLink may identify the homologous zebrafish sequence.
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• follow provided Links from Entrez Gene >> Entrez Protein or HomoloGene
• The Entrez Protein record includes a link to the pre-computed protein comparisons in BLink (BLAST link)
2. How do I find my gene ? • for example: the SIX1 gene has been identified in human.
• Look for related zebrafish sequences (from the Links menu) in HomoloGene (via related UniGene clusters) or Entrez Protein (via related proteins identified in BLink)
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2. How do I find my gene ? BLink: BLAST link• BLink provides protein BLAST results between your query protein and all Entrez proteins
• Look at the list of proteins, click on the “Best hits” button to view a list of the number of hits for each organism
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91% Identical
• BLink results for the human SIX1 protein identifies
a highly similar (91% identical ) zebrafish protein
• click on the protein Accession to go to Entrez Protein
• click on the Score to view the BLAST2 protein alignment
2. How do I find my gene ? BLink: BLAST link
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2. How do I find my gene ? • view the Entrez Protein record
• from the pull-down Links menu, choose the Link to Entrez Gene to view the Gene record
associated with the zebrafish protein identified via the BLink comparison
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2. How do I find my gene ? • the Entrez Gene record details page provides links to external source of the data (e.g. ZFIN) and links to other Entrez databases (e.g. PubMed)
• Entrez Gene records are continually updated.
• This record was updated to six1 30-Jul-2004.
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2. How do I find my gene ? • functional information can be submitted to the Entrez Gene record via the GeneRIF submission form
www.ncbi.nlm.nih.gov/RefSeq
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2. How do I find my gene ? www.sanger.ac.uk/Projects/D_rerio
starting with cDNA/EST/peptide sequences
• BLAST/SSAHA servers for Vega and EnsEMBL
• BLAST server for (un-)finished clones
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2. How do I find my gene ? www.sanger.ac.uk/Projects/D_rerio
starting with a gene name
• text search in Vega and EnsEMBL
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2. How do I find my gene ? www.sanger.ac.uk/Projects/D_rerio
starting with a homologuous gene
• EnsEMBL gene from different species ‘Orthologue Prediction’
• example: human FOXN4 gene
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2. How do I find my gene ? www.sanger.ac.uk/Projects/D_rerio
starting with a marker or genomic position (clone)
• in EnsEMBL via text search or ‘mapsearch’
• in Vega via text search
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2. How do I find my gene ? www.sanger.ac.uk/Projects/D_rerio
how to obtain gene sequences
• in Vega and EnsEMBL: mouse overs
• in Vega and EnsEMBL: data downloads (‘Export Data’)
• in EnsEMBL: general downloads (pre-computed datasets from mainpage)
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2. How do I find my gene ? www.sanger.ac.uk/Projects/D_rerio
how to create on-the-fly datasets
• in EnsEMBL: EnsMART at www.ensembl.org/Multi/martview
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available gene information
• in EnsEMBL and Vega: GeneView with link to ZFIN
2. How do I find my gene ? www.sanger.ac.uk/Projects/D_rerio
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zebrafish
at the Sanger Institute, ZFIN and NCBI
3. How do I find gene-related data ?
Gene abc
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3. How do I find gene-related data ? www.sanger.ac.uk/Projects/D_rerio
inferring gene function
• in EnsEMBL and Vega: GeneView textual entries (description, homologues,
orthologues)
• supporting evidence (‘Exon Information’)
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finding homologues in other species
• in EnsEMBL: ‘Orthologue Prediction’
• in EnsEMBL: Compara tracks with sequence comparison
3. How do I find gene-related data? www.sanger.ac.uk/Projects/D_rerio
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3. How do I find gene-related data ? www.sanger.ac.uk/Projects/D_rerio
genomic context
• in EnsEMBL and Vega: ContigView pages
• with SNPs, affymetrix mapping, translated-BLAT comparisons to other species
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3. How do I find gene-related data ? www.sanger.ac.uk/Projects/D_rerio
physical map (FPC database)
• mapping information, start with one clone and browse
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3. How do I find gene-related data ? www.sanger.ac.uk/Projects/D_rerio
ordering clones
• help on ‘frequently asked questions’ page
• can also be found on library details page (mapping)
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Where do I find approved nomenclature ?3. How do I find gene-related data ?
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Where do I find approved nomenclature ?3. How do I find gene-related data ?
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How might I infer gene function ?3. How do I find gene-related data ?
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How might I infer gene function ?3. How do I find gene-related data ?
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How might I infer gene function ?3. How do I find gene-related data ?
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How might I infer gene function ?3. How do I find gene-related data ?
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How do I find gene expression data ?
gbx2
3. How do I find gene-related data ?
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How do I find gene expression data ?3. How do I find gene-related data ?
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How do I find gene expression data ?3. How do I find gene-related data ?
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How do I find gene expression data ?3. How do I find gene-related data ?
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How do I find gene expression data ?3. How do I find gene-related data ?
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Where do I find relevant clones ?3. How do I find gene-related data ?
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Where do I find relevant clones ?3. How do I find gene-related data ?
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Where do I find sequence information ?3. How do I find gene-related data ?
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Where do I find sequence information ?3. How do I find gene-related data ?
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Where do I find sequence information ? 3. How do I find gene-related data ?
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Where do I find sequence information ?3. How do I find gene-related data ?
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Where do I find sequence information ? 3. How do I find gene-related data ?
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Where do I find sequence information ?3. How do I find gene-related data ?
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Has my gene been mapped ?3. How do I find gene-related data ?
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Has my gene been mapped ?3. How do I find gene-related data ?
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Are there known orthologues for my gene ?3. How do I find gene-related data ?
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Are there known orthologues for my gene ?3. How do I find gene-related data ?
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What publications discuss my gene ?3. How do I find gene-related data ?
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What phenotypic data is available ?3. How do I find gene-related data ?
ti282a
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What phenotypic data is available ?3. How do I find gene-related data ?
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What phenotypic data is available ?3. How do I find gene-related data ?
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• submit BLAST searches of nucleotide or protein sequences
• submit genome-specific BLAST searches
3. How do I find gene-related data ? www.ncbi.nlm.nih.gov/BLAST Where do I find related sequences ? How do I find members of a gene family ?
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3. How do I find gene-related data ? http://www.ncbi.nlm.nih.gov/genome/seq/DrBlast.html
• submit BLAST searches against zebrafish databases
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• the Map Viewer home page provides links to organism–specific map data where you can query to find a marker or gene, query against the entire genome, or link to view markers mapped to a particular chromosome
3. How do I find gene-related data ? www.ncbi.nlm.nih.gov/mapviewIs my gene mapped ? How do I find my gene by map position ? What markers are mapped near my gene ?
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3. How do I find gene-related data ? www.ncbi.nlm.nih.gov/mapview
• submit a search against genetic or RH maps
• refine your search by options in the Advanced Search page
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3. How do I find gene-related data ? www.ncbi.nlm.nih.gov/mapviewHow do I find all mapped members of a gene family ?
• results are displayed as hits on each Linkage Group and in a table of hits per Linkage Group
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• Advanced search page allows you to restrict queries by LG, object type or map
3. How do I find gene-related data ? www.ncbi.nlm.nih.gov/mapview
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3. How do I find gene-related data ? www.ncbi.nlm.nih.gov/mapviewWhat markers are mapped near my gene ? Where do I find map-related data ?
• navigate between Linkage Groups at the top of the page
• add/remove maps, or change options by clicking Maps & Options
• view marker placement along a chromosome or LG
• navigate to ZFIN, Entrez Gene, UniSTS by provided links
• view connections (red lines) between maps
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3. How do I find gene-related data ? www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=SnpAre there SNPs associated with my gene ?
• view SNP, genotype and population details • query dbSNP by snp_gene[filter]
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zebrafish
at NCBI, the Sanger Institute and ZFIN
2. Where can I get help or ask questions?
?
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• contact the NCBI help desk at [email protected]
• submit suggestions to Entrez Gene’s suggestion form
4. Where can I ask questions or submit suggestions ?
www.ncbi.nlm.nih.gov/RefSeq/update.cgi
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4 . How can I get help ? www.sanger.ac.uk/Projects/D_rerio
• ‘frequently asked questions’ page
• email [email protected]
• extensive documentation for ensembl at www.ensembl.org
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4. Where can I ask questions or submit suggestions ?
Comments or Questions:
Visit our booth in the exhibitors hall
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www.ncbi.nlm.nih.gov/genome/guide/zebrafish/Workshop2004
NCBI: www.ncbi.nlm.nih.gov
ZFIN: zfin.org
Sanger: www.sanger.ac.uk/Projects/D_rerio/
Acknowledgements
NCBIDonna Maglott Kim Pruitt Greg Schuler Deanna Church Wonhee Jang Lukas Wagner Joan Pontius Carolyn ShenmenEd Lee Cliff Clausen RefSeq Curators Map Viewer Developers
ZFINMonte Westerfield Dave Clements Tom Conlin David FashenaKen Frazer Sherry GigliaMelissa Haendel Doug HowePrita Mani Sridhar RamachandranKevin Schaper Erik SegerdellPeiran Song Brock SprungerSierra Taylor Ceri Van Slyke
Sanger InstituteMario CaccamoTim HubbardJane RogersEnsEMBL teamVega teamSean Humphrayand the mapping team
Zemin Ning and the high performance assembly team
web team sequencing teams
Genome Resources Workshop
