Zebrafish Genome Resources Workshop

1. Zebrafish Genome Resources Workshop Mario Caccamo - Sanger Institute Judy Sprague - ZFIN Lynn Schriml - NCBI

2. Genome Guide page: to see what is new for zebrafish -- LInk to our workshop and module at Sanger NCBI home page: to see what is new throughout NCBI NCBI home page announcements of what is new, navigation our user community consists of individuals retrieving data via our web browsers and large scale data extractors: via eutils and ftp files Zebrafish Genome Browser and Genome Annotation at NCBI -annotation of Sangers assembly - genome data at NCBI, ftp files, Trace Archive, download - genome placement info propegated to other NCBI resources Spline : align mRNAs to the genome Entrez: expanded : new databases, new Book domains of information we have, we are a public repository, please make those deposits Gene: BIND data MyNCBI Customized Display of Search Results and Search Results Emails UniGene expanded: Expression Data, virtual northerns Links to other similarily expressed clusters or homologous clusters (via HomoloGene results) Genome Resource Pages: Projects database and Genome Guide Pages -database of sequencing and mapping projects -guide for web resources Genome Guide page: to see what is new for zebrafish -- LInk to our workshop and module at Sanger NCBI home page: to see what is new throughout NCBI NCBI home page announcements of what is new, navigation our user community consists of individuals retrieving data via our web browsers and large scale data extractors: via eutils and ftp files Zebrafish Genome Browser and Genome Annotation at NCBI -annotation of Sangers assembly - genome data at NCBI, ftp files, Trace Archive, download - genome placement info propegated to other NCBI resources Spline : align mRNAs to the genome Entrez: expanded : new databases, new Book domains of information we have, we are a public repository, please make those deposits Gene: BIND data MyNCBI Customized Display of Search Results and Search Results Emails UniGene expanded: Expression Data, virtual northerns Links to other similarily expressed clusters or homologous clusters (via HomoloGene results) Genome Resource Pages: Projects database and Genome Guide Pages -database of sequencing and mapping projects -guide for web resources

4. One of the biggest “NEW” things at NCBI for Zebraifsh, The zebraifsh genome has joined out family of annotatied organisms. We have annoated the Sanger assembly, currently Zv4, soon Zv5. Here is the our process, input alignments and blasts placing objects on to the genome feedback loops products of the annotation ADDING CONTEXT TO THE GENOME Identify objects to be annotated defined by sequence computed from sequence An ongoing process Use our own heuristics/comparisons, place our objects on the genome Genome Annotation: Provides: Reference transcripts (models, genes, marker), pseudogenes and proteins annotated on the genome and in GenBank files (SHOW GenBank file with the annotation) Assimilates data from numerous sources Places known genes and other data in genomic context Predicts new genes Links annotation to other resources Reveals informative relationships -- show genetic, RH and Genome sequence in one browswer One of the biggest “NEW” things at NCBI for Zebraifsh, The zebraifsh genome has joined out family of annotatied organisms. We have annoated the Sanger assembly, currently Zv4, soon Zv5. Here is the our process, input alignments and blasts placing objects on to the genome feedback loops products of the annotation ADDING CONTEXT TO THE GENOME Identify objects to be annotated defined by sequence computed from sequence An ongoing process Use our own heuristics/comparisons, place our objects on the genome Genome Annotation: Provides: Reference transcripts (models, genes, marker), pseudogenes and proteins annotated on the genome and in GenBank files (SHOW GenBank file with the annotation) Assimilates data from numerous sources Places known genes and other data in genomic context Predicts new genes Links annotation to other resources Reveals informative relationships -- show genetic, RH and Genome sequence in one browswer

5. How can I align mRNAs to the genome ? computes transcript alignments for genome annotation use the online version to submit an accession for alignment download and install Spline (major platforms) Cross-species mode computes transcript alignments for genome annotation use the online version to submit an accession for alignment download and install Spline (major platforms) Cross-species mode

6. Where can I BLAST Zebrafish sequences ? --here is one of the products We have added the genome sequence to our zebrafish blast page, where you can submit a BLAST against any of these zebrafish databases -- get here from BLAST home page--here is one of the products We have added the genome sequence to our zebrafish blast page, where you can submit a BLAST against any of these zebrafish databases -- get here from BLAST home page

7. a graphical display display placement of objects display links to related information/data In external data bases (e.g. ZFIN) or Entrez Databases options: view data as graphical display, in a table, download the sequence or ftp files, Advanced Options: Maps and Options: a graphical display display placement of objects display links to related information/data In external data bases (e.g. ZFIN) or Entrez Databases options: view data as graphical display, in a table, download the sequence or ftp files, Advanced Options: Maps and Options:

8. Point out ways to access the data, via: this web browser download the sequnce see it in a text view ftp files Point out ways to access the data, via: this web browser download the sequnce see it in a text view ftp files

12. New book chapter Genome projects My NCBI: Figure Tab Customized Display of Search Results and Search Results Emails: MyNCBI New book chapter Genome projects My NCBI: Figure Tab Customized Display of Search Results and Search Results Emails: MyNCBI

14. 1.UniGene, MyNCBI tabs Choosing one UniGene Cluster 2. Links Pull down menu, to view related records in these other databases, UniGene_homologous: to see putative homologs identified by HomoloGene database See Expression data: compare experimental expression results in ZFIN with UniGene’s Expression profile based the clusters ESTs 3. Scroll down to view these ESTs and the mRNAs that comprise the cluster 4. Click on Expression profile 5. UniGene expanded: Expression Data, virtual northerns Links to other similarily expressed clusters or homologous clusters (via HomoloGene results) 1.UniGene, MyNCBI tabs Choosing one UniGene Cluster 2. Links Pull down menu, to view related records in these other databases, UniGene_homologous: to see putative homologs identified by HomoloGene database See Expression data: compare experimental expression results in ZFIN with UniGene’s Expression profile based the clusters ESTs 3. Scroll down to view these ESTs and the mRNAs that comprise the cluster 4. Click on Expression profile 5. UniGene expanded: Expression Data, virtual northerns Links to other similarily expressed clusters or homologous clusters (via HomoloGene results)

16. Acknowledgements