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If this is the first time you're installing Office you may have some setup steps to do first. Expand the learn more section below. However, if you're reinstalling Office, and you've already redeemed a product key and have an account associated with Office, then go to the section sign in and install Office on your PC or Mac. FinchTV is the popular way to view sequence traces on Linux, Mac OSX, and Windows. FinchTV is the only trace viewer that can display an entire trace in a scalable multi-pane view. FinchTV reads chromatogram files from the most popular formats. In addition to displaying a multi-color sequence above the trace, FinchTV displays quality values (when available).
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2021-2022 WSSP Lecture Notes, Presentations, and Videos
This web page provides links to materials for the Waksman Student Scholars Program for the 2021-2022 academic year. This information is intended for the students and faculty participating in the program during the 2021 Summer Institute and through the 2021-2022 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. | 2021-2022 Lecture Topics Student Links | Notes | Videos (.mp4) | Figures (.pdf) | Figures (.ppt) |
|---|---|---|---|---|---|
| Introduction to the vWSSP21 Summer Institute | Mtg.mp4 | ||||
| Introduction and overview of project | Ch0 | ||||
0 | Polymers and DNA Structure | ||||
| Vectors: Plasmids, Libraries, and DNA preps Background on Vectors Background on Libraries Plasmid DNA Minipreps | Ch.1A Ch.1B Ch.1C | ||||
| PCR, Mapping the size of an insert Background on PCR Analysis of an agarose gel of the PCR samples | Ch.2A Ch.2B | ||||
| 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 | ||||
| DNA Sequencing, | Ch.4 | ||||
| Logging onto DSAP, Sequence quality, crop ends DSAP & Bioinformatic Analysis Overview Determine waveform quality Analysis of a poor waveform Cropping the waveform | Ch.5A Ch.5B Ch.5C Ch.5D | ||||
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 Q2-5. DSAP tables on the BLASTn searches | Ch.7A Ch.7B Ch.7C | |||
8 | BLASTX (Translated DNA vs Protein search) BLASTx Background Q1-4. Performing a BLASTx seach on the NCBI nr database Analysis of Frameshifts | Ch.8A Ch.8B Ch.8C | |||
9 | Determining ORFs, BLASTP (Protein vs Protein search) Overview of ORF Determination, BLASTP, UTRs Using Toolbox to Determine the ORF Using NCBI ORFfinder to Determine the ORF Performing the BLASTP search Comparison of the BLASTX vs BLASTP data Review Page: Determining the 5' and 3' UTRs | Videos Ch.9A Ch.9B1 Ch.9B2 Ch.9C Ch.9D Ch.9E | |||
10 | Literature Search | Ch.10 | |||
| 11A | Search for a human homolog | Ch.10B | Ch.11(A) | ||
11B | Compare Insert Sizes (Only if you purified your own clones) | Ch.11 | |||
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 TAIR or NCBI BLASTp search for Arabidopsis Homologs: Steps Search of the BioGRID Database: Steps | Ch. 14 | Ch.14A Ch.14B | Ch14.pdf | Ch14.ppt |
| 15 | Expression and Localization Analysis Expression Studies on the eFP Browser Localization Studies on the Cell efP BRowser | Ch. 15 | Ch.15A Ch.15B | Ch15.pdf | Ch15.ppt |
| 16 | Molecular Biology Expts.: What to do next | Ch. 16 | Ch.16A Ch.16B | Ch16.pdf | Ch16.ppt |
| 17 | Multiple Sequence alignment CLUSTALW (optional) | Ch.17 | Ch17.pdf | Ch17.ppt | |
| 18 | Analysis of REV sequences (optional) Rev Sequence Quality Rev Sequence Insert Start Rev Sequence Insert End | Ch.18a | Ch18.pdf | ||
| 19 | Spanning the gap (optional) | Ch. 19 | Ch19.pdf | Ch19.ppt | |
| 20 | JMol and Protein Modeling (optional) | Ch20.ppt | |||
| 21 | Preparing a poster (optional) |
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List of DNA Sequence Waveform Viewers can be found here