Genome Editing with Apollo

Slides:



Advertisements
Similar presentations
EAnnot: A genome annotation tool using experimental evidence Aniko Sabo & Li Ding Genome Sequencing Center Washington University, St. Louis.
Advertisements

Genomics: READING genome sequences ASSEMBLY of the sequence ANNOTATION of the sequence carry out dideoxy sequencing connect seqs. to make whole chromosomes.
Visualization of genomic data Genome browsers. UCSC browser Ensembl browser Others ? Survey.
Tutorial 7 Genome browser. Free, open source, on-line broswer for genomes Contains ~100 genomes, from nematodes to human. Many tools that can be used.
Alignment of mRNAs to genomic DNA Sequence Martin Berglund Khanh Huy Bui Md. Asaduzzaman Jean-Luc Leblond.
Visualization of genomic data Genome browsers. How many have used a genome browser ? UCSC browser ? Ensembl browser ? Others ? survey.
BME 130 – Genomes Lecture 7 Genome Annotation I – Gene finding & function predictions.
Gene Finding Charles Yan.
Visualization of genomic data Genome browsers. UCSC browser Ensembl browser Others ? Survey.
Genome Annotation BCB 660 October 20, From Carson Holt.
Lecture Objectives Define Terms: Transcription, Translation, nucleic acid, amino acid, DNA, RNA, mRNA, cDNA, “ATCG”, Gene, Genomics, Protein, Proteomics,
Doug Brutlag 2011 Genome Databases Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University School of Medicine Genomics, Bioinformatics.
Chapter 6 Gene Prediction: Finding Genes in the Human Genome.
Using DNA Subway in the Classroom Red Line Lesson Sketch.
Alternative Splicing. mRNA Splicing During RNA processing internal segments are removed from the transcript and the remaining segments spliced together.
Using DNA Subway in the Classroom Red Line Lesson Sketch.
Progress report Yiming Zhang 02/10/2012. All AS events in ASIP Intron retention Exon skipping Alternative Acceptor site NAGNAG AltA Alternative Donor.
Genome Annotation using MAKER-P at iPlant Collaboration with Mark Yandell Lab (University of Utah) iPlant: Josh Stein (CSHL) Matt Vaughn.
Bikash Shakya Emma Lang Jorge Diaz.  BLASTx entire sequence against 9 plant genomes. RepeatMasker  55.47% repetitive sequences  82.5% retroelements.
 GEP Digital Laboratory Notebook Nick Reeves, Mt. San Jacinto Community College.
Use cases for Tools at the Bovine Genome Database Apollo and Bovine QTL viewer.
GeneWise and Artemis Exercises Spliced Alignment using GeneWise Click on the GeneWise hyperlink on the course links page,
Sequence & course material repository Annotation (sequences & evidence) Manuals (DNA, Subway, Apollo, JalView) Presentations.
Welcome to DNA Subway Classroom-friendly Bioinformatics.
Browsing the Genome Using Genome Browsers to Visualize and Mine Data.
1 Transcript modeling Brent lab. 2 Overview Of Entertainment  Gene prediction Jeltje van Baren  Improving gene prediction with tiling arrays Aaron Tenney.
Review of Protein Synthesis. Fig TRANSCRIPTION TRANSLATION DNA mRNA Ribosome Polypeptide (a) Bacterial cell Nuclear envelope TRANSCRIPTION RNA PROCESSING.
LECTURE CONNECTIONS 14 | RNA Molecules and RNA Processing © 2009 W. H. Freeman and Company.
Sackler Medical School
Mark D. Adams Dept. of Genetics 9/10/04
Eukaryotic Gene Prediction Rui Alves. How are eukaryotic genes different? DNA RNA Pol mRNA Ryb Protein.
Figure S1. Figure S2 (a) Figure S2 (b) Figure S2 (c)
How can we find genes? Search for them Look them up.
Research about Alternative Splicing recently 楊佳熒.
Web Apollo Resources at the National Agricultural Library Christopher Childers NAL ARS USDA i5k.nal.usda.gov.
Bioinformatics Workshops 1 & 2 1. use of public database/search sites - range of data and access methods - interpretation of search results - understanding.
-1- Module 3: RNA-Seq Module 3 BAMView Introduction Recently, the use of new sequencing technologies (pyrosequencing, Illumina-Solexa) have produced large.
UCSC Genome Browser Zeevik Melamed & Dror Hollander Gil Ast Lab Sackler Medical School.
Exercise 3 Inspecting the primary structure of a gene.
Gene Finding in Chimpanzee Evidence based improvement of ab initio gene predictions Chris Shaffer06/2009.
AP Biology Chapter 17. RNA Processing AP Biology Transcription -- another look The process of transcription includes many points.
A knowledge-based approach to integrated genome annotation Michael Brent Washington University.
Visualization of genomic data Genome browsers. How many have used a genome browser ? UCSC browser ? Ensembl browser ? Others ? survey.
Visualization of genomic data Genome browsers. UCSC browser Ensembl browser Others ? Survey.
Alternative Splicing. mRNA Splicing During RNA processing internal segments are removed from the transcript and the remaining segments spliced together.
Using public resources to understand associations Dr Luke Jostins Wellcome Trust Advanced Courses; Genomic Epidemiology in Africa, 21 st – 26 th June 2015.
Using DNA Subway in the Classroom Genome Annotation: Red Line.
Molecular Genetics - From DNA to Trait Traits DNA To.
Genetic Code and Interrupted Gene Chapter 4. Genetic Code and Interrupted Gene Aala A. Abulfaraj.
Alternative Splicing. mRNA Splicing During RNA processing internal segments are removed from the transcript and the remaining segments spliced together.
1 Gene Finding. 2 “The Central Dogma” TranscriptionTranslation RNA Protein.
318 bp insertion between Exon 2 and 3
bacteria and eukaryotes
Annotating The data.
Using DNA Subway in the Classroom
Daphnia Genome Preview at wFleaBase.org
Detect alternative splicing
Visualization of genomic data
Visualization of genomic data
Gene Annotation with DNA Subway
Ensembl Genome Repository.
Gene Sizes Vary Strachan p146 DYSTROPHIN.
Gene Sizes Vary Strachan p146 DYSTROPHIN.
Reading Frames and ORF’s
4. HMMs for gene finding HMM Ability to model grammar
Introduction to Alternative Splicing and my research report
Part II SeqViewer AraCyc Help
KIT Gene Deletions at the Intron 10−Exon 11 Boundary in GI Stromal Tumors  Christopher L. Corless, Laura McGreevey, Ajia Town, Arin Schroeder, Troy Bainbridge,
DNA Crash course…..
BRCA1 protein functional domains and predicted frameshift and premature truncation. BRCA1 protein functional domains and predicted frameshift and premature.
Presentation transcript:

Genome Editing with Apollo

5 times (32x zoom)

Which of the predictions appears supported by the biological evidence?

Examine your gene model: Does it agree with the biological evidence Examine your gene model: Does it agree with the biological evidence? Does it have a start and stop codon? Are the splice sites ok?

Fix the UTRs, Name it, Upload it.

Delete Exon

Split Exon

Delete Blastn model Name your Gene model Upload to DNA subway

What is going on here? New Track- User BLASTn data- EST and cDNA data

Done! Time for St. Nick Ewing!