Posts by: Debbie
Expired MTAs
Written by on Oct. 24, 2023 .
October SEA-PHAGES Email
Written by on Oct. 9, 2023 .
Archiving Information 2021-22
Written by , on Oct. 15, 2021 .
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 ...
Archiving 2018
Written by on Oct. 16, 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 ...
Auto-annotation Fix for DNA Master
Written by on Oct. 27, 2017 .
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
Written by on Nov. 16, 2016 .
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 ...
2016 Fall Archive Tubes
Written by on Nov. 1, 2016 .
Archive tubes were shipped this week. Expect them no later than Thursday, November 3, 2016.
Annotation Guide for School Year 2015-16
Written by on Nov. 23, 2015 .
Annotation: What's new in 2014-15?
Written by on Jan. 13, 2015 .
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 ...
2014 In Silico Workshop
Written by on Dec. 16, 2014 .
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!