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Introduction to VectorNTI September 14, 2011

Introduction to VectorNTI September 14, 2011. Ansuman Chattopadhyay , PhD, Head Molecular Biology Information Service Health Sciences Library System University of Pittsburgh ansuman@pitt.edu http://www.hsls.pitt.edu/guides/genetics. Topics. Vector NTI Advance 11.0 Suite Overview

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Introduction to VectorNTI September 14, 2011

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  1. Introduction to VectorNTISeptember 14, 2011 AnsumanChattopadhyay, PhD, Head Molecular Biology Information Service Health Sciences Library System University of Pittsburgh ansuman@pitt.edu http://www.hsls.pitt.edu/guides/genetics

  2. Topics • Vector NTI Advance 11.0 Suite Overview • How to Import or Create New Sequences • Sequence Alignments: AlignX • Sequence Assembly: ContigExpress • Analyze Sequences: PCR and Primers, Restrictions and Mutagenesis • How to create Vector Maps

  3. Video Tutorials • VectorNTI user inter phase : a short walk-through • http://media.hsls.pitt.edu/media/clres2705/vnti_walkthrough_part1.swf (16 min) • http://media.hsls.pitt.edu/media/clres2705/vnti_walkthrough_part2.swf (10 min) • Import your DNA of interest into VectorNTI • http://media.hsls.pitt.edu/media/clres2705/vnti_inportdna.swf(14 min ) • Create a multiple protein sequences alignment plot • http://media.hsls.pitt.edu/media/clres2705/vnti_msa.swf (17 min) • Design PCR primers using VectorNTI • http://media.hsls.pitt.edu/media/clres2705/vnti_pcr.swf (11 min) • Clone a fragment from pBR322 into pUC19 (in sillicomolecule construction) • http://media.hsls.pitt.edu/media/clres2705/vnti_cloning.swf (15 min)

  4. Exercise • PLCg1: • Mouse: NP_067255 • Rat: NP_037319 • Cow: NP_776850 • Dog: XP_542998 • Zebra fish: NP_919388 • Human: NP_002651 • NP_067255,NP_037319,NP_776850,XP_542998,NP_919388,NP_002651

  5. Important Links • PowerPoint Guide to Molecule Construction and Design • PowerPoint Guide to Managing the Vector NTI Database • Northwestern University VectorNTI tutorial

  6. A Molecule Construction Example • Task – Clone a fragment from pBR322 into pUC19 ☼Donor fragment: pBR322, 5’EcoRI—3’AvaI ☼Recipient fragment: pUC19, 5’SmaI—3’EcoRI • Getting started 1. Open pBR322 and pUC19 in Vector NTI 2. Arrange the display window to display 2 molecules on the same screen: ☺Select Menu > Window > Tile Vertical

  7. Hands - On • Epidermal Growth Factor receptor is considered as one of the bio-markers for several forms of cancer including Breast and Ovarian cancers. • Create a Vector NTI file for the gene EGFR (Accession Number: P00533 ) • Design PCR primers to amplify any one domain of your choice present in EGFR protein.

  8. Thank you!Any questions? Carrie Iwema Ansuman Chattopadhyay iwema@pitt.eduansuman@pitt.edu 412-383-6887 412-648-1297 http://www.hsls.pitt.edu/guides/genetics

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