Zebrafish Genome Resources Workshop

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Zebrafish Genome Resources Workshop

• Mario Caccamo - Sanger Institute
• Judy Sprague - ZFIN
• Lynn Schriml - NCBI

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Whats new at NCBI ?
www.ncbi.nih.gov
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Whats new at NCBI for zebrafish?
www.ncbi.nih.gov/genome/guide/zebrafish/
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Zebrafish Genome Annotated at NCBI
STS
dbSNP
Clones
Gnomon models
GenBank
Entrez Gene
RefSeqs
Align with BLAST hits and Splign
Resource Updates
Assembly
Zv4 genome sequence and assembly
instructions from the Sanger Institute
Public Release
Annotation products
GenBank Records updated FTP files BLAST
databases Map Viewer Genome Browser
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How can I align mRNAs to the
genome ?
A tool for producing spliced global
alignmentsYuri Kapustin, Alexandre Souvorov,
Tatiana Tatusova David Lipman
TARGET
QUERY
www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi
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Where can I BLAST Zebrafish sequences ?
BC053166 BC055621
www.ncbi.nlm.nih.gov/genome/seq/DrBlast.html
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Map Viewer Genome Browser query maps and the
genome

• Search and display genomic information by
  chromosome position

• Retrieve regions or objects of interest by text
  queries (gene or marker name) or by sequence
  alignment (BLAST)

• View results at whole genome level

• Select objects to display

www.ncbi.nlm.nih.gov/mapview/
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MapViewer Advanced Search and Results
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MapViewer view marker placement on maps or the
genome
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MapViewer choose maps to display, zoom in or out
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MapViewer view transcripts aligned to the genome
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What are the new Entrez databases ?
axis formation AND Danio rerioorganism
New book chapter Genome projects My NCBI Figure
Tab
www.ncbi.nlm.nih.gov/gquery/gquery.fcgi
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Where is my gene expressed ?
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Acknowledgements
The Zebrafish Information Network The Wellcome
Trust Sanger Institute
Garth Brown Mark Cavanaugh
Slava Chetvernin
Hsiu-Chuan Chen Deanna Church Karen
Clark
Cliff Clausen Olya Ermolaeva
Jennifer
Hart Wratko Hlavina Wonhee
Jang Paul Kitts
Melissa Landrum
Donna Maglott Peter Meric
Kim Pruitt Bhanu Rajput
Sergey Resenchuk Barbara Ruef Victor
Sapojnikov Greg Schuler
Steve Sherry
Aleksey Virokurov
Lukas Wagner Jack Wang
Janet
Weber
National Center for Biotechnology Information
(NCBI) National Library of Medicine National
Institutes of Health
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Zebrafish Genome Resources Workshop Dresden
2005
-- a hands-on self guided tour of Sanger, ZFIN
and NCBI resources --
1. Where do I start?

• Zebrafish Genome Sequencing Page (Sanger)
• ZFIN home page (ZFIN)
• Zebrafish Genome Resources, NCBI home page (NCBI)

2. Maps and Genome Sequence

• Ensembl genome browser (Sanger)
• Vega Browser (Sanger)
• Map Viewer (NCBI)
• How do I find a zebrafish gene in the genome ?

3. Genes and Sequences

• How do I find information about a gene ?
  (NCBI,ZFIN)
• Does my gene have know homologues/orthologs ?
• How can I find cDNA clones for my gene ? (ZFIN)
• What can I find about a ZGC clone and its
  proteins ? (NCBI)
• Data mining in Ensembl with EnsMart (Sanger)

4. Function and Expression

• How do I determine gene function ? (NCBI, ZFIN)
• Expression patterns ? (ZFIN)
• Can I find a molecular marker for a given
  anatomical structure ? (ZFIN)

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Are there sequencing and mapping projects for
zebrafish ?