Bioinformatics caacaagccaaaactcgtacaaCgagatatctcttggaaaaactgctcacaatattgacgtacaaggttgttcatgaaactttcggtaAcaatcgttgacattgcgacctaatacagcccagcaagcagaat Managing.

Slides:

Advertisements

Similar presentations

Parallel BioInformatics Sathish Vadhiyar. Parallel Bioinformatics  Many large scale applications in bioinformatics – sequence search, alignment, construction.

Advertisements

Test practice Multiplication. Multiplication 9x2.

Reference mapping and variant detection Peter Tsai Bioinformatics Institute, University of Auckland.

          Sequence Analysis with Artemis and.

Dawei Lin, Ph.D. Director, Bioinformatics Core UC Davis Genome Center July 20, 2008, SLIMS (Solexa sequencing.

MARCUS LYON Bioinformatics Workshop Why I’m Here Gain a better understanding of bioinformatics  Benefit my current/future research  Useful information.

Sequence Analysis MUPGRET June workshops. Today What can you do with the sequence? What can you do with the ESTs? The case of SNP and Indel.

General methods of SNP discovery: PolyBayes Gabor T. Marth Department of Biology Boston College Chestnut Hill, MA

NHGRI/NCBI Short-Read Archive: Data Retrieval Gabor T. Marth Boston College Biology Department NCBI/NHGRI Short-Read.

Bio 465 Summary. Overview Conserved DNA Conserved DNA Drug Targets, TreeSAAP Drug Targets, TreeSAAP Next Generation Sequencing Next Generation Sequencing.

Sequence Alignment Oct 9, 2002 Joon Lee Genomics & Computational Biology.

Sequence Variation Informatics Gabor T. Marth Department of Biology, Boston College BI420 – Introduction to Bioinformatics.

Genome Assembly Bonnie Hurwitz Graduate student TMPL.

Sequence comparison: Local alignment

DNA Sequencing. Fig

Mapping NGS sequences to a reference genome. Why? Resequencing studies (DNA) – Structural variation – SNP identification RNAseq – Mapping transcripts.

Todd J. Treangen, Steven L. Salzberg

Transcriptome analysis With a reference – Challenging due to size and complexity of datasets – Many tools available, driven by biomedical research – GATK.

Phred/Phrap/Consed Analysis A User’s View Arthur Gruber International Training Course on Bioinformatics Applied to Genomic Studies Rio de Janeiro 2001.

1 Overview of HDF5 HDF Summit Boeing Seattle The HDF Group (THG) September 19, 2006.

GBS Bioinformatics Pipeline(s) Overview

June 11, 2013 Intro to Bioinformatics – Assembling a Transcriptome Tom Doak Carrie Ganote National Center for Genome Analysis Support.

Multiple Sequence Alignments  Assemble DNA sequences into a ‘contig’  Identify conserved residues and domains.

Next Generation DNA Sequencing

MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads Hua Bao Sun Yat-sen University, Guangzhou,

By Zemin Ning & Adam Spargo Informatics Division The Wellcome Trust Sanger Institute The SSAHA2 Application Pack.

Genomics (BIO 426) James Madison University. Why are you here? Have you taught Genomics before? Plan to teach it soon? Might you teach it sometime? Just.

Advancing Science with DNA Sequence Metagenome definitions: a refresher course Natalia Ivanova MGM Workshop September 12, 2012.

RNA Sequencing I: De novo RNAseq

RNA-Seq Assembly 转录组拼接唐海宝基因组与生物技术研究中心 2013 年 11 月 23 日.

Next Generation Sequencing pipeline: a joint LONI – BIRN [UCLA – UCI] collaborative project F. Macciardi – March 16, 2011.

Current Challenges in Metagenomics: an Overview Chandan Pal 17 th December, GoBiG Meeting.

AutoEditor Automated base caller error correction tool Slides courtesy of Pawel Gajer, Ph.D.

Bioinformatics Scheme of the sequencing project (Martínez & Figueras, 2007) Construction Bookseller Bases determination Fragments assembly Gene search.

MICROARRAY TECHNOLOGY

Data Workflow Overview Genomics High- Throughput Facility Genome Analyzer IIx Institute for Genomics and Bioinformatics Computation Resources Storage Capacity.

Plant Biology Division Post-process of IMGAG M.t. 2.0 Release Affymetrix Medicago Probe set – IMGAG 2.0 / MTGI 8.0 Mapping Zhao Bioinformatics Lab.

Accessing and visualizing genomics data

GSVCaller – R-based computational framework for detection and annotation of short sequence variations in the human genome Vasily V. Grinev Associate Professor.

Chapter 5 Sequence Assembly: Assembling the Human Genome.

454 Genome Sequence Assembly and Analysis HC70AL S Brandon Le & Min Chen.

L ESSON A IMS & O BJECTIVES Two part lab: First part will be completed in class today. (1) Use the online Bioinformatics tool ClustalW to analyze DNA sequences.

Assembly S.O.P. Overlap Layout Consensus. Reference Assembly 1.Align reads to a reference sequence 2.??? 3.PROFIT!!!!!

Short Read Workshop Day 5: Mapping and Visualization

A brief guide to sequencing Dr Gavin Band Wellcome Trust Advanced Courses; Genomic Epidemiology in Africa, 21 st – 26 th June 2015 Africa Centre for Health.

DNA Questions What makes up a DNA backbone? How would you describe how DNA looks? Name the 4 bases that make up DNA. “T” base can only match with? What.

From Reads to Results Exome-seq analysis at CCBR

Lesson: Sequence processing

HDF5 Metadata and Page Buffering

Reads aligned into contigs

Ssaha_pileup - a SNP/indel detection pipeline from new sequencing data

Sequence comparison: Local alignment

Human Cells Human genomics

Example of a common SNP in dogs

GEP Annotation Workflow

Predicting Active Site Residue Annotations in the Pfam Database

2nd (Next) Generation Sequencing

Discovery tools for human genetic variations

Bioinformatics: Buzzword or Discipline (???)

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Identify D. melanogaster ortholog

CISC 667 Intro to Bioinformatics (Spring 2007) Review session for Mid-Term CISC667, S07, Lec14, Liao.

Analysis of the Influence of Computer Technology in Nutrigenomics

Genome Biology & Applied Bioinformatics Mehmet Tevfik DORAK, MD PhD

Basic Local Alignment Search Tool (BLAST)

Polymorphism discovery in 09-CB1 × IPO323 versus 09-ASA-3apz × IPO94269 bulks. Polymorphism discovery in 09-CB1 × IPO323 versus 09-ASA-3apz × IPO94269.

Assembly of Solexa tomato reads

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Presentation transcript:

Bioinformatics caacaagccaaaactcgtacaaCgagatatctcttggaaaaactgctcacaatattgacgtacaaggttgttcatgaaactttcggtaAcaatcgttgacattgcgacctaatacagcccagcaagcagaat Managing genomic data

Nov. 29, 2006HDF Workshop X, Landover MD2 DNA sequencing workflows Diverse formats Redundant data Repeated file processing In-core processing models Lack of persistence

Nov. 29, 2006HDF Workshop X, Landover MD3 Multiple Levels of Information Contig Summaries Discrepancies Contig Qualities Coverage Depth Read quality Aligned bases Contig Reads Percent match Trace SNP Score

Nov. 29, 2006HDF Workshop X, Landover MD4 HDF5 as format for bioinformatics