Contact info

1

• Contact info
• pierre_at_biol.sc.edu
• 803-777-8703
• Web site
• http//www.scinbre.org/program/bioinformatics-core
  .html

2
Vector NTI user manual

• Difficult to use 758 pages!
• First chapters tutorial on a few modules.
• Complete description of all the functionalities
  (customization)
• Online tutorial (only on a few modules)

3
Presentation of the workshop

• Installation of the package
• Brief description of the modules
• Vector NTI databases
• VectorNTI (display, primers, cloning strategies,
  gel display)
• Other modules (AlignX, Contig Express,
  GenomBench)
• Live demo, hands-on practice

4
Installation

• Download the package
• https//catalog.invitrogen.com/index.cfm?fuseactio
  nuserGroup.downloadCenter
• https//catalog.invitrogen.com/index.cfm?fuseactio
  nuserGroup.userGroupHome
• Register to vector NTI user community
• Request a license (need a PO number)

5
Easy to install
6
2 types of licenses
7
Renew after one year
8
Register your license number
9
Vector NTI advance10

• Vector NTI Explorer (databases)
• Vector NTI (molecule display, gel display,
  analyses)
• AlignX (multiple sequence alignment)
• ContigExpress (generate contigs)
• Analysis Monitor
• Pubmed-Entrez Search
• BLAST Search
• BioAnnotator (DNA/prot biochemical analysis)
• GenomBench (genome display)
• 3D Molecule Viewer

10
Vector NTI Explorer
11
8 databases
12

• Import/add data
• Search databases
• Work on databases

13
Import/add data

• (Not working on demo version)

14
Import data from files
Drag
15
Import restriction enzymes
16
Add new restriction enzyme
17
Add new oligo
18
Import oligo data
User manual p686
Name, sequence, description
19
Add new gel marker
20
Add new citation
21
Import Pubmed search output
(Working in demo)
22
Use of citation database
(Working in demo)
Right click
23
Search databases
24
Search nucleotide databases
25
Search protein databases
26
Search enzyme database
27
Search oligo database
28
Search gel marker database
29
Search citation database
30
Search blast results database
31
Work on database
32
Create a database subset
Right click
33
Define a user field
34
Add a field in the display
Right click
35
Edit an entry
36
Database display options
37
Exercise 1

• Open main nucleotide database
• Search molecules with CDS AP(R)
• Create a user field Amp. Res.
• list of predefined string (Amp. Res)
• Set Amp. Res. to search subset
• Add Amp. Res. field in the database table
• Sort database on Amp. Res.