Links

SGD Home

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SGD Resource Links

SGD Cohort Schedule

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SGD Contact Information

SGD Faculty Workshop

 

KBRIN SGD Resources

Acknowledgement

The resources used in the Small Genome Discovery program were initially developed by Dr. Graham Hatful’s lab at the University of Pittsburgh as part of the PHIRE program. As a Howard Hughes Medical Institute (HHMI) fellow, he was asked to incorporate his program into the Science Education Alliance (SEA) National Genome Research Initiative (NGRI), which later became the Phage Hunters Advancing Genomics and Evolutionary Science (PHAGES) program.  These resources have been used by permission to expand the PHAGES program to institutions within the Commonwealth of Kentucky.

Protocols

In situ protocols

In silico protocols

 

Phagesdb.org

The phagesdb.org database is the site into which your students will deposit their phage EM pictures, plaque pictures, isolation location and site description, DNA restriction enzyme digest gel pictures and their phage’s name. This database holds information on over 4699 phages and the sequence for over 672 phage genomes.

All of the resources are available online at phagesdb.org under the Resources and Software menus.

A very nice glossary of phage terms can be found under the Resources/Glossary menu of phagesdb.org.

Phagehunting Procedures & Protocols

Software
            DNA Master – is a genome annotation and exploration tool.
            Phamerator – a genome exploration and comparison tool.
            AceUtil – a genome quality assessment and finishing tool.
            Aaragorn – an online tRNA identification program.
            tRNAscan-SE – an online tRNA identification program.

Other documentation, software guides, annotation resources, and powerpoint presentations can also be found under the Resources/Documentation menu of phagesdb.org.

The HHMI SEA also has a wiki with useful information and conversations.

If you would like to see what other schools are also participating in the PHAGES program, click on the Resources/Institutions menu link in phagesdb.org. There are currently over 122 institutions participating in this program.