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

Posts by: Debbie

Expired MTAs

Action needed if you do not have a current MTA for materials sent to you for phagehunting.

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October SEA-PHAGES Email

Important requests/timelines for Phage Discovery

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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 ...

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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 ...

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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 ...

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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 ...

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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! 

Upcoming Events

Annual SEA Faculty Meeting

June 7, 2024 to June 10, 2024

2024 SEA Faculty Meeting

June 7, 2024 to June 10, 2024

Phage Discovery Workshop 17A

June 22, 2024 to June 28, 2024

Recent Events

2024 SEA Symposium

April 12, 2024 to April 14, 2024

2024 SEA Symposium

April 12, 2024 to April 14, 2024

Forum Activity

Debbie Jacobs-Sera posted in spanins

Shallee Page posted in spanins

pia1@pitt.edu posted in GeneMarkS ?

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