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

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Annotation

If your question fits into one of the sub-forums below, please post it there. If not, create a new topic on this page.
Forums Topics Posts Last post
SMART Function Investigations
As SMART proceeds through their functional assignment investigations, they will share how and what they find, and post it here. Use these investigations to develop your investigations in your classrooms for deeper understanding of phage biology.
3 7 Jun 3, 2025
1:18 PM
Choosing Start Sites
Questions about tricky-to-call start sites.
17 75 Jun 3, 2025
12:08 PM
tRNAs
Questions about properly searching for and calling tRNAs.
26 103 Sep 30, 2024
7:37 AM
Functional Annotation
Questions about whether or not to call functions, or precisely how to call them.
155 572 May 13, 2025
11:06 AM
Gene or not a Gene
Questions about whether or not to call or delete certain genes.
36 133 Feb 4, 2025
1:09 AM
Frameshifts and Introns
This forum is for asking questions about annotatiing frameshifts in the tail assembly chaperone genes and intron boundaries in Cluster J phages.
26 112 Jun 16, 2025
9:40 AM
Request a new function on the SEA-PHAGES official list
56 196 Jun 12, 2025
2:15 PM
Notes and Final Files
Questions about required notes in DNA Master and submitting final annotation files.
23 98 Jan 20, 2025
7:14 PM
How to Pass Preliminary Annotation Review
2 6 May 1, 2023
9:14 AM
HHpred
Questions about how to use or interpret results from HHpred.
0 0
Topics Posts Views Last post
2022 Genomics Workshop Follow-up Annotation: Ciao pages: 1 2
13 123 Jan 17, 2023
9:11 AM
TAC in FM cluster
6 32 Apr 10, 2022
3:29 PM
Called an orpham but isn't?
5 21 Apr 6, 2022
2:28 PM
Capsid genes
1 16 Apr 6, 2022
1:49 PM
duplicated genes at start/end of genome
6 36 Apr 6, 2022
12:44 PM
In Genbank
9 68 Feb 18, 2022
12:30 PM
New function? Hfq RNA binding protein
7 57 Feb 15, 2022
1:22 PM
Phosphoribosyl transferase new function: Phelipe_64 and Bosnia_40
1 11 Feb 4, 2022
3:16 PM
Is this a sequencing error?
3 19 Jul 15, 2021
10:32 AM
Mid-gene deletion causing frameshift and orphams
6 237 Jun 3, 2021
10:19 AM
List of bioinformatic software
2 472 May 18, 2021
1:13 PM
ORPHAMs
2 23 Mar 3, 2021
12:25 PM
Phage Predator (H1) mis-annotation of lysin A gene?
3 23 Feb 18, 2021
8:35 PM
% alignment
2 14 Feb 15, 2021
12:07 PM
Tape measure in K1 phage
3 58 Jan 12, 2021
4:10 PM
Phage Jinkies - error in annotation?
3 30 Nov 17, 2020
2:51 PM
PE/PPE proteins
1 19 Jul 28, 2020
5:37 PM
sigma factors & transcription factors
1 17 May 30, 2020
11:50 AM
Function for Gene 1 of EK1 Phages
7 79 May 21, 2020
4:36 PM
Having trouble getting NCBI Blast data for a gene via …
3 20 May 10, 2020
3:38 PM

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