Speaker: Shih-Chieh Lin

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An Integrated Tool of Bioinformatics-Vector NTI
??????????

• Speaker Shih-Chieh Lin

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Why should I use Vector NTI ?

• User friendly
• Consistent Multi-Interface Pane Interface in All
  Applications
• Easy to understand
• Easy to manage
• Powerful Illustration Tools for Publication
  Quality Graphics

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What can Vector NTI help you ?

• Sequence annotation
• Compare sequence results
• Help you design primer
• Verify your original sequence result
• Map construction

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Sequence Annotation
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Forward 1 Reverse 1 amplify Wild type
Variant 1 (113 229 bp) Forward 2 Reverse 2
amplify Wild type Variant 2 (504 162 bp )
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Application of AlignX
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Map Construction
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Introduction

• How to use Vector NTI
• How to annotate and analyze your sequence ?
• Primer design and Oligo analyze
• AlignX
• Contig Express
• How to construct your map

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Function of Vector NTI

• BioAnotator
• AlignX
• Contig Express

• Blast Search
• PubMed Search
• Citation Viewer
• 3-D Mol

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Vector NTI web-resource

• http//www.basic.northwestern.edu/VectorNTI/Docume
  ntation/VectorNTI/
• http//www.invitrogen.com/content.cfm?pageid10352

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?? ?? ? ???? InforMax ? Vector NTI Suite 8.0
?Vector NTI Explorer
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?????
?????
???Database???
????? Subbases
??Database?????
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1.???????? add Separator????????????? 2.?????? ?
????????New Subbase ?????????
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?????????Sequence file?Vector NTI Database
Method One Copy Past
????Vector NTI Explorer???Table?
??New????Molecule
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??Molecule???????????Sequence??????DNA/RNA
Molecule
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????????????? Sequences andMaps
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??? Edit Sequence
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???Sequence???????OK???????????Sequence file
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Method Two Retrieve from NCBI
?NCBI Search??Nucleotide????????????????
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??????Genomic region, transcripts, and products
??? NM ID ???GENEBANK??????
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???? Download ??? GenBank?????????
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???Vector NTI Explorer?? Import ??? Molecule from
Text file??? GenBank??OK
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?????????file??? ????????????Subbase
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?????????Subbase???OK??????????????
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????Vector NTI
???
???
???
? ? ?
? ? ?
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????????? ??????PPT or Word
????
Text pane
Add feature
????????????????
Picture pane
?? Setup
Sequence pane
Find Sequence
Molecule Setup
?????????? ? pane ??
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How to annotate your sequence ?
1.???????Annotate???
?? Edit???? Find Sequence (????????Sequence??,Find
Sequence???????)
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? sequence ?????? Find Next?????????? (????????Seq
uence??,Find Sequence???????)
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??? Edit??? New? ?? add Feature To Map ?????
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2.???Annotate??????????
??????
Rrverse???? ?????????
?????????
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????,??????annotate???,????????????????
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???sequence?????????????????????????????? ? Save
As Files????????????Vector NTI database (?????????
?????????????,??add feature ???????)
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????
??Save As File ?????????????? (
????????sequence??????????modify)
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??Insert Sequence
Ex?insert region
????????Insert?????? New ? ??? Insert
Sequence?????
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???Insert?sequence? ??OK??
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Predict Restriction Site in your sequence
????Vector NTI Explorer? ????? Enzymes????list????
RE Enzymes????????? lab???? vector RE subbase
???????????subbase???
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????Vector NTI?? Analyzes ? Restriction Analyzes
? Restriction sites
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????
??add ? ???????? ,??????? ????enzymes
database?? ???????Vector RE subbase? select all
????
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??????????????????? Restriction Enzymes
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How to analyze your sequence?
?? Analyzes? BioAnnoator ?Analyze Selected
Molecule
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?????????? ?? Analyzes ????Analyzes List
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List ?????????????? ???????????? ??????????
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Primer Design
???????Primer ?region?????????Analyzes?Primer
Design ? Find PCR Primers
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??????????????????????????????????? ?
?????????Primer? 5??? Restriction site
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????????Text pane?,????????Primer
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Design Sequencing primer
???????Primer ?region?????????Analyzes?Primer
Design ? Sequenceing Primers
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Primer ??????
?????????sequencing region ???????OK???????????
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How to analyze your primer ?
???
? PCR primer result??????? Analyzes
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???????? Analyzes? ?????????
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???(????????Paired Primer or oligo)
? PCR primer result??????? Add To Oligo List
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?Primer??????? ?? (????Reverse ?Primer???)
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????Oligo List?????????????????List ?????????????(
??????)
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????????Primer???Analyzes????????Primer
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??????Primer???????,??Shift????????????Duplexes ??
????Oligo Duplexes?????Analyzes
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???
???????????????????Primer???????Primer Dimer
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How to use AlignX ?
?Vector NTI Explorer??????align?????
?????Align ?AlignX-Align Selected Molecule
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????
???
????align???? ??Align ?Align Selected Sequences
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???????????? Camera?????????PPT or
Word ???Display Setup ???Alignment???? ?
??Feature Type Color Scheme ???????
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???????????? Find Sequence??????????????
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????????,????????????????????????
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?? Align???? Show Similarity Tables
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????Similarity??? ? ????????????? PPT or Word ?
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How to use Contig Express ?
???Vector NTI Explorer???Assemble? ???
ContigExpress-Open New Assemble Project
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??????E-mail???Sequence result file??????????
ContigExpress ?? ??? Project???? add Fragments
??? From ABI file
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?????? All Files ??? Sequence result files ?????
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?????????????????? ??? ?
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????? ??? Edit ? ??????????
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????? ??? Open? ??????sequence result file
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Sequence result
?????????
???????????
Signal of sequence result
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????? ??? Copy? ?? Vector NTI Explorer? Paste
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???????????? Make reverse complement?????
Reverse???
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?????????????? Copy ???Vector NTI Explorer
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??? Paste???? Align????????????,Check sequence???
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How to Construct your Map ?
?????Vector Sequence import?Vector NTI
explorer(?????Vector,???????? ??????),???Data
sheet ?Vector? Annotation,????????Vector?Restricti
on site? Subbase
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?????Primer?5???? insert Vector??Restriction
site?? Edit??Insert ?? (?????????Insert
sequence????Restriction Enzyme)
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????????? insert? RE site? Ex ???Kpn I??? shift
??Bgl II, ?? ???? insert sequence
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First select
Second select
?????????????? add Fragment to Goal List
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???????????insert ? Fragment List? (??????)
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Second select
First select
???? Vector?? ????Bgl II???Shift???Kpn I (?????
RE site?????Insert sequence???????????Vector??)
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??????????
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???????????? Vector ?sequence???Fragment List?
(??????)
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??????????????????????Fragment????Run(??????)
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??????????Name???????,???????Map??????Construct
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???????????????????Vector? subbase?????OK
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???????Construct Map???????Insert sequence
??????Annotation
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??????????? ???Camera???Map????PPT or
Word? ???Graphics Display Setup???annotate???? ???
Edit picture???????
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??????????????????????Molecule???Save as
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?????
???Save in DNA/RNA Molecule Databases?????????????
???subbase
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?????
????Save As File ?????????????? (
????????sequence??????????modify)
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Thank you for your attention