Culturable Bacterial Communities Analyzer DIANA VANESSA SARRIA-ZUNIGA ELIANA TORRES-ZELADA April 29, 2016.

Slides:

Advertisements

Similar presentations

In Silico Primer Design and Simulation for Targeted High Throughput Sequencing I519 – FALL 2010 Adam Thomas, Kanishka Jain, Tulip Nandu.

Advertisements

Enter Presentation Everything you expect …plus DNASIS MAX 2.0 Sequence Analysis Software.

Mutation Analysis Server Nagarajanlab. © Copyright 2005, Washington University School of Medicine. 2 Agenda Mutation pipeline overview High level design.

Lettuce genetic map viewer is written in PHP and uses GD library. The viewer interacts with tables in the relational mySQL database and creates graphical.

Homework Assignments due next session 1.Find a entry of interest in OMIM ( )

Perl Practical Extraction and Report Language Senior Projects II Jeff Wilson.

Space/Time Tradeoff and Heuristic Approaches in Pairwise Alignment.

Bioinformatics Workshop.  We started by discussing what bioinformatics is and how it is used  We learned that DNA is the information about an organism.

Bioinformatics for the Canadian Potato Genome Project David De Koeyer, Martin Lagüe and Rebecca Griffiths Wageningen September 18, 2004.

Advanced Perl for Bioinformatics Lecture 5. Regular expressions - review You can put the pattern you want to match between //, bind the pattern to the.

How to use the web for bioinformatics Molecular Technologies February 11, 2005 Ethan Strauss X 1373

Visual Basic and Perl Applications for Genome Project Management. Svetlana N.Yurgel* 1, Brenda K. Schroeder 1, Hao Jin 2 and Michael L. Kahn 1,3. Institute.

I.1 ii.2 iii.3 iv.4 1+1=. i.1 ii.2 iii.3 iv.4 1+1=

Introduction to Bioinformatics - Tutorial no. 5 MEME – Discovering motifs in sequences MAST – Searching for motifs in databanks TRANSFAC – The Transcription.

MICB 405 Bioinformatics Mini-Lab #2 - BLAST Dr. Joanne Fox We gratefully acknowledge the funding for the development of these teaching.

I.1 ii.2 iii.3 iv.4 1+1=. i.1 ii.2 iii.3 iv.4 1+1=

A Novel Third Isoform of Zebrafish Cytochrome Oxidase IV Brandon Smith Dr. Nancy Bachman, Faculty Advisor.

Sequence Analysis. DNA and Protein sequences are biological information that are well suited for computer analysis Fundamental Axiom: homologous sequences.

Zachary Bendiks. Jonathan Eisen  UC Davis Genome Center  Lab focus: “Our work focuses on genomic basis for the origin of novelty in microorganisms (how.

Advanced Perl for Bioinformatics Lecture 5. Regular expressions - review You can put the pattern you want to match between //, bind the pattern to the.

DNA BARCODING CHILLIES BIO-NERDS : Say Wah Yugraj Singh Tanja Obradovic Jenny Pham Lovita Bharossa Buai Chuol Diana Corzo.

Basic Introduction of BLAST Jundi Wang School of Computing CSC691 09/08/2013.

Student Learning Environment on the World Wide Web l CGI-programming in Perl for the connection of databases over the Internet. l Web authoring using Frontpage.

MCB 5472 Psi BLAST, Perl: Arrays, Loops, Hashes J. Peter Gogarten Office: BPB 404 phone: ,

MCB 5472 Assignment #6: HMMER and using perl to perform repetitive tasks February 26, 2014.

Collecting and Storing Sequences In the laboratory Heather Helm UPR Sequencing Facilities Manager.

Gao Song 2010/07/14. Outline Overview of Metagenomices Current Assemblers Genovo Assembly.

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

Information System for Comparative Analysis of Legume Genomes Anita Dalwani Advisors: Dr. Roger Innes, Dr. Haixu Tang.

Regulatory Genomics Lab Saurabh Sinha Regulatory Genomics Lab v1 | Saurabh Sinha1 Powerpoint by Casey Hanson.

Pyrosequencing for Metagenomics: accessing and organizing raw data Giuseppe D’Auria FISABIO, Valencia Norwich September 2014.

Module 3 Sequence and Protein Analysis (Using web-based tools) Working with Pathogen Genomes - Uruguay 2008.

Denovo genome assembly and analysis

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

Using SWARM service to run a Grid based EST Sequence Assembly Karthik Narayan Primary Advisor : Dr. Geoffrey Fox 1.

Overview of Bioinformatics 1 Module Denis Manley..

Regulatory Genomics Lab Saurabh Sinha Regulatory Genomics | Saurabh Sinha | PowerPoint by Casey Hanson.

Parsing BLAST output. Output of a local BLAST search “less” program Full path to the BLAST output file.

BioPerl Ketan Mane SLIS, IU. BioPerl Perl and now BioPerl -- Why ??? Availability Advantages for Bioinformatics.

PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors.

SAGExplore web server tutorial. The SAGExplore server has three different modules …

__________________________________________________________________________________________________ Fall 2015GCBA 815 __________________________________________________________________________________________________.

Today House Keeping (talks, sequencing) Follow-up on cloning

Introduction to Bioinformatics - Tutorial no. 5 MEME – Discovering motifs in sequences MAST – Searching for motifs in databanks TRANSFAC – the Transcription.

PICODIV database and web site status in May 2001.

Chapter 5 Sequence Assembly: Assembling the Human Genome.

Metagenomic dataset preprocessing – data reduction

Dept. of Animal Breeding and Genetics Programming basics & introduction to PERL Mats Pettersson.

HANDS-ON ConSurf! Web-Server: The ConSurf webserver.

PROTEIN IDENTIFIER IAN ROBERTS JOSEPH INFANTI NICOLE FERRARO.

MESA A Simple Microarray Data Management Server. General MESA is a prototype web-based database solution for the massive amounts of initial data generated.

Robert Edgar Independent scientist

Barcode sequences at GenBank

MGmapper A tool to map MetaGenomics data

Core Elements Engineering - Midrange

Regulatory Genomics Lab

EDNA analyze Wang Ying & Huang Junman.

Reads aligned into contigs

Genotyping and Bioinformatics Comparison between Sanger and 454

ACL SCREEN Start with Standard ACL Project Screen.

Workshop on the analysis of microbial sequence data using ARB

Lecture 4: Probe & primer design

Strategy for F1 mutation carrier screening and identification of their mutations. Strategy for F1 mutation carrier screening and identification of their.

Using MATLAB to identify genes in novel genomes based on homology

Comparative Genomics.

Rotation review Gaurav Moghe Genetics Program

Identification of Bacteria BBT203 Ach

Multiple sequence alignment & Phylogenetics Analysis

Regulatory Genomics Lab

Regulatory Genomics Lab

Presentation transcript:

Culturable Bacterial Communities Analyzer DIANA VANESSA SARRIA-ZUNIGA ELIANA TORRES-ZELADA April 29, 2016

Bacterial 16S rRNA Modified from: sequence-analysis PCR amplification of region V3-V6 Modified from: 2. Sanger sequencing PCR product V3-V6

REQUIREMENTS: 1.Access to Purdue servers 2.Access to Purdue Bioinformatics Core facility: -module perl/ module CAP3/ module muscle/ module mothur/ module usearch/ GAST ( Global Assignment of Sequence Taxonomy for SSU rRNA ) files

1. DOWNLOAD: TRIMMED SEQUENCES AND QUALITY SCORE FILES Trimmed sequences Quality score file LWP::UserAgent Screen scrapping  links

2. ASSEMBLY CAP3 FORWARD AND REVERSE COMPLEMENT SEQUENCES  CONTIGS Perl script: Reverse complement One file per sample  Run CAP3 per sample  Store all contigs in one file

3. ALIGNMENT MUSCLE: ALIGN CONTIGS TO SEARCH REGION V3, V6 AND V3-V6 Perl Script: search primers V3F, V3R, V6F, V6R and extract the three regions Input: contigs  MUSCLE  Output: Alignment of contigs

4. TAXONOMY ASSIGNMENT GAST File with all regions V3 File with all regions V6 OUTPUT GAST

6. DATABASE MySQL One table i. Colony ID ii. Taxonomy GAST Region V3: Domain;Phylum;Class;Order;Family;Genus;Species iii. Taxonomy GAST Region V6 Domain;Phylum;Class;Order;Family;Genus;Species. iv. BLAST Region V3-V6 v. Final Taxonomy 5. FINAL IDENTIFICATION Perl script: compare taxonomy assigned for V3 and V6 region of each colony. If they agree  final identification. If they do not agree  submit the V3-V6 fasta file to BLAST and keep the best 5 hits.

THANK YOU QUESTIO NS??