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Resources for Students

2017-2018 WSSP Lecture Notes, Presentations, and Videos

This web page provides links to materials for the Waksman Student Scholars Program for 2017. This information is intended for the students and faculty participating in the program during the 201. summer institute and through the 2017-2018 academic year. It is not intended for general public use and access is password protected. The material on these pages is provided for educational purposes only. Unauthorized use of this material is prohibited. If you are not a member of the WSSP and wish to download the files or have comments or questions about the material please contact Sue Coletta, Waksman Institute, Rutgers University.

Ch. 2017 Lecture Topics Student Links
 
Notes 
(.pdf)
Videos
(.mp4)
Figures 
(.pdf)
Figures 
(.ppt)
0
Introduction and overview of project   Ch0
0
Polymers and DNA Structure    
1
Vectors: Plasmids, Libraries, and DNA preps
   Background on Vectors
   Background on Libraries
   Plasmid DNA Minipreps
 
Ch.1a
Ch1.b
Ch1.c
2
PCR, Mapping the size of an insert
   Background on PCR
   Analysis of an agarose gel of the PCR samples
 
Ch.2a
Ch.2b
3
Restriction enzymes, Mapping the size of an insert
   Background on Restriction Enzymes
   Analysis of an agarose gel of the Restriction Digest samples
 
Ch.3a
Ch.3b
4
DNA Sequencing,   Ch.4
5
Logging onto DSAP, Sequence quality, crop ends
   Determine waveform quality
   Analysis of a poor waveform
   Determining where the cDNA insert starts
   Determining where the cDNA insert ends​
   Cropping the waveform
 
Ch.5a
Ch.5b
Ch.5c
Ch.5d
Ch.5e
6
Editing the waveform Ch.6
7
BLASTN (DNA vs DNA search)
   Q1a. Performing a BLASTn seach of nr
   Q1b. Analyzing the NCBI BLASTn results
   Q2. DSAP table on the BLASTn searches
   Q3-4 BLASTn Search of EST
   Q5-6. Similarity Questions
  
Ch.7a
Ch.7b
Ch.7c
Ch.7d
Ch.7e
8
BLASTX (Translated DNA vs Protein search)
   BLASTx Overview
   Q1. Performing a BLASTx seach on the NCBI nr database
   Q2-4. Analyzing the NCBI BLASTn results
 
Ch.8a
Ch.8b
Ch.8c
9
Determining ORFs, BLASTP (Protein vs Protein search)
   Overview
   ORF Analysis Steps
   BLASTp Analysis
   Comparing BLASTx vs BLASTP data
   DSAP Review Page Steps
 
Ch.9a
Ch.9b
Ch.9c
Ch.9d
Ch.9e
10
Literature Search
   Literature Search
   Search for a human homolog
 
Ch.10a
Ch.10b
11
Multiple Sequence alignment CLUSTALW  
12
PDB Search for Homologous Proteins  Ch.12 
13 Next Gen Sequencing and TSA Search
   Background
   Steps
Ch. 13  
Ch.13a
Ch.13b
Ch13.pdf Ch.13.ppt
14 Searching for Protein Interactions
   Background
   Steps
Ch. 14  
Ch.14a
Ch.14b
Ch14.pdf Ch14.ppt
15 Molecular Biology Expts.:  What to do next Ch. 15 Ch.15 Ch15.pdf Ch15.ppt
16 Analysis of REV sequences (optional)
   Rev Sequence Quality
   Rev Sequence Insert Start
   Rev Sequence Insert End
   Determine For & Rev Overlap
   Edit Alignments
   Form a Contig

Ch.16a
Ch.16b
Ch.16c
Ch.16d
Ch.16e
Ch.16f

Ch16.pdf
17 Spanning the gap (optional) Ch. 17   Ch17.pdf Ch17.ppt
18 JMol and Protein Modeling (optional)   Ch18.ppt
19 Preparing a poster  (optional)    

Parental Release Form (doc) (pdf)

Download FinchTV (external site)   Download FinchTV (from WSSP site)

Download 4Peaks