SEA-PHAGES Logo

The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

Posts by: Debbie

Archiving Information 2021-22

The procedure for sending archiving samples to the University of Pittsburgh is largely similar this year, but please read carefully.

Note that you do not need to add beads to tubes anymore.

Contact Us/Questions

Please send any questions about the information below to Debbie (djs@pitt.edu) and Becky (rag4@pitt.edu).

Please read the latest Archiving Instructions ...

Continue reading

Archiving 2018

Archive tubes and boxes will go out the week of November 5, 2018.  If you have not entered your section data, please do so.  If you have a special need, please let debbie know (djs@pitt.edu).  Please re-familiarize yourself with the archving protocol in the PhageDiscovery Guide of your choice. Remember that archiving is as much ...

Continue reading

Auto-annotation Fix for DNA Master

Recently, NCBI changed accessibility to Glimmer and GeneMark servers. Upon update and a few key re-configurations, DNA Master can once again auto-annotate. Please follow the directions in the attached document to get auto-annotation working again. Yay!

How to update DNA Master to restore auto-annotation functionality

debbie

DNA Master Updated to Use Secure NCBI Connections

Thanks to Jeffrey Lawrence, significant changes have been made to the DNA Master code which now allow it to access the newly-secure servers of NCBI. To obtain these changes, you need to update the program. Without updating, important features of DNA Master will not work, including auto-annotation and BLASTing.

To update, open DNA Master ...

Continue reading

2016 Fall Archive Tubes

Archive tubes were shipped this week. Expect them no later than Thursday, November 3, 2016.

Annotation Guide for School Year 2015-16

We are not making any changes to the Annotation Guide for school year 2015-16. So the current edition is available and ready for printing at PhagesDB. The What’s New document is now ready too! Happy Annotating!

Annotation: What's new in 2014-15?

The revised DNA Master Annotation Guide is available on PhagesDB and the sea-wiki.  Below are some important revisions to note.

  • The process for submitting genomes for annotation QC has changed slightly.  You are asked to submit two .dnam5 files.  Particular attention to functional calls is needed.
  • Start-site decision-making has been modified to use the Karlin/Kaplan ...

Continue reading

2014 In Silico Workshop

If you are interested in the In Silico Workshop materials you can find them at PhagesDB.

To all the participants, may we commend you on a job well done!!!  The GenBank Accession number for Mycobacteriophage Sheen is KP273225! 

"Life in Our Phage World"

"Life in Our Phage World"

Check out this new book (and free pdf) about phages.  It may just be the ticket for that quirky, informative approach to phage background you are looking for!

From the 2015phage.org website:  "To celebrate a century of phage exploration, we invite you to get intimate with 30 diverse phages in this premier phage field guide. ...

Continue reading

Archiving 2014-15

We are shipping tubes for archiving on November 5, 2014.  The number of tubes you will receive will depend on the number of students enrolled in your classes that you enter on seaphages.org.  Please do so by October 29, 2014.  Once you have entered your student numbers and shipping address, we will have ...

Continue reading

Upcoming Events

Cohort 14 Phage Genomics Workshop (Dec 2021)

December 6, 2021 to December 17, 2021

Recent Events

2021 GENES Faculty Workshop

June 15, 2021 to June 16, 2021

Forum Activity

afreise posted in Question about notes template

Debbie Jacobs-Sera posted in Question about notes template

dwilliams posted in Question about notes template

FORUMS HOME PAGE