Genome Resources Workshop · 2004. 11. 8. · Genome Resources Workshop Genes Genome Sequence Map...

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 ?

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

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

• 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

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

• the Genome Biology page provides links to organism specific resource pages

1. Where do I start ? www.ncbi.nlm.nih.gov

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

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.

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

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

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

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

1. Where do I start ? www.sanger.ac.uk/Projects/D_rerio

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

zfin.org

Zebrafish Model Organism DatabaseZFIN

Gene Products Gene Expression

Mutant Phenotypes

Sequence InformationMapping Data

Orthology

zfin.org

zebrafish

at ZFIN, NCBI and the Sanger Institute

Gene xyz

zfin.org

Genomic ContextMapping Panels

Whole Genome Sequence

• 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/

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.

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

• 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.

• 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)

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

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

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

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.

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

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

starting with a gene name

• text search in Vega and EnsEMBL

starting with a homologuous gene

• EnsEMBL gene from different species ‘Orthologue Prediction’

• example: human FOXN4 gene

starting with a marker or genomic position (clone)

• in EnsEMBL via text search or ‘mapsearch’

• in Vega via text search

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)

how to create on-the-fly datasets

• in EnsEMBL: EnsMART at www.ensembl.org/Multi/martview

available gene information

• in EnsEMBL and Vega: GeneView with link to ZFIN

zebrafish

at the Sanger Institute, ZFIN and NCBI

Gene abc

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’)

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

genomic context

• in EnsEMBL and Vega: ContigView pages

• with SNPs, affymetrix mapping, translated-BLAT comparisons to other species

physical map (FPC database)

• mapping information, start with one clone and browse

ordering clones

• help on ‘frequently asked questions’ page

• can also be found on library details page (mapping)

zfin.org

Where do I find approved nomenclature ?3. How do I find gene-related data ?

zfin.org

Where do I find approved nomenclature ?3. How do I find gene-related data ?

zfin.org

How might I infer gene function ?3. How do I find gene-related data ?

zfin.org

How do I find gene expression data ?

zfin.org

How do I find gene expression data ?3. How do I find gene-related data ?

zfin.org

Where do I find relevant clones ?3. How do I find gene-related data ?

zfin.org

Where do I find relevant clones ?3. How do I find gene-related data ?

zfin.org

Where do I find sequence information ?3. How do I find gene-related data ?

zfin.org

Where do I find sequence information ? 3. How do I find gene-related data ?

zfin.org

Where do I find sequence information ? 3. How do I find gene-related data ?

zfin.org

Has my gene been mapped ?3. How do I find gene-related data ?

zfin.org

Has my gene been mapped ?3. How do I find gene-related data ?

zfin.org

Are there known orthologues for my gene ?3. How do I find gene-related data ?

zfin.org

Are there known orthologues for my gene ?3. How do I find gene-related data ?

zfin.org

What publications discuss my gene ?3. How do I find gene-related data ?

zfin.org

What phenotypic data is available ?3. How do I find gene-related data ?

ti282a

zfin.org

• 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 ?

3. How do I find gene-related data ? http://www.ncbi.nlm.nih.gov/genome/seq/DrBlast.html

• submit BLAST searches against zebrafish databases

• 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 ?

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

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

• 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

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

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]

zebrafish

at NCBI, the Sanger Institute and ZFIN

2. Where can I get help or ask questions?

• contact the NCBI help desk at info@ncbi.nlm.nih.gov

• submit suggestions to Entrez Gene’s suggestion form

www.ncbi.nlm.nih.gov/RefSeq/update.cgi

4 . How can I get help ? www.sanger.ac.uk/Projects/D_rerio

• ‘frequently asked questions’ page

• email zfish-help@sanger.ac.uk

• extensive documentation for ensembl at www.ensembl.org

zfin.org

Comments or Questions:

zfinadmn@zfin.org

Visit our booth in the exhibitors hall

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

Genome Resources Workshop · 2004. 11. 8. · Genome Resources Workshop Genes Genome Sequence Map...

Documents

NCBI FieldGuide A Field Guide part 2 Genome resources Sequence similarity Apr, 2007 Shandong University

NCBI FieldGuide A Minimal Guide to NCBI Nucleotide Resources

Introduction to NCBI

Melampsora Genome Annotation and Genome Structure Analysis First Annotation Workshop of the Melampsora Genome Consortium Yao-Cheng Lin Bioinformatics &

RPA-Based Method For The Detection Of SARS-CoV2...2020/09/17 · Primer design was based on the complete genome sequence of the SARS CoV2 isolate Wuhan-Hu-1, complete genome, NCBI

ncbi pcos 2009

UCSC Genome Browser Workshop (pdf)

NCBI Field Guide NCBI Molecular Biology Resources March 2007 NCBI Databases

NCBI BLASTaz12722.vo.msecnd.net/hpcazurebursttrainingcourse1 … · Web viewDownload and extract the human genome database files from the NCBI FTP server: Browse to the NCBI FTP server

Using NCBI

NCBI Handbook

NCBI FieldGuide NCBI Molecular Biology Resources January 2008 Using Entrez

NCBI FieldGuide NCBI Molecular Biology Resources March 2007 Using Entrez

Introduction Why is human genetics important? The family history The human genome project On the web The human genome NCBI Other web sites Outline

MYNCBI-LOG · NCBI Resources How To (9 Sign in to NCBI My NCBI retains user information and database preferences to provide customized services for many NCBI databases. Goole and

Unilag workshop complex genome analysis

INAM's NCBI Handbook

Genome representation and variant identification Deanna M. Church, NCBI

Introduction Why is human genetics important? The human genome project On the web The human genome NCBI Other web sites Outline

Mol. Phylogenet. Evol. Mol. Biol. Whole-genome analyses ...science.sciencemag.org/content/sci/346/6215/1320.full.pdf · (NCBI), and ENSEMBL (NCBI and Ensembl accession numbers are