Link to this post | posted 31 Oct, 2024 20:19
Tamarah_Adair	Thank you! I appreciate your quick response.

Link to this post | posted 31 Oct, 2024 15:52

Tamarah_Adair

I am working on MRAs and these are one of the reviewer's comments: – Illumina platform description and a description of how the reads were quality controlled is missing - Line 46: versions used should be added (Newbler and Consed) - a description of how the genome termini were determined is lacking, This is the paragraph I submitted Genomic DNA was isolated using the Wizard® DNA Clean-Up Kit (Promega) and sequenced by the Pittsburg Bacteriophage Institute using Illumina Sequencing. The NEB Ultra II Library Kit, v3 reagents, was used for each phage with read lengths recorded at 150-base single-end reads. The number of reads and average sequence coverage is recorded in Table 1. Reads were assembled using Newbler (8 ) and Consed (9). Any help is much appreciated. Tammy Edited 31 Oct, 2024 17:01

Link to this post | posted 31 Oct, 2024 14:39
Tamarah_Adair	Thanks for posting. I am having the same issue.

Link to this post | posted 13 Jan, 2024 20:08

Tamarah_Adair

Vassie, I was thinking the same thing about the shirts! David, thank you for all the inspiring messages and leadership. I will miss seeing you, but I wish you the very best! Tammy vcw0 Dear David, There is not a word big enough yet in languages I know to account for the impact you have had on the Science Education community and me. I thank you for all the inspiration and advice you provided that powered us forward with this work. I wish you all the peace and adventure you can handle. Just one question remains - what do I do with all the Hawaiian shirts I ordered over the holidays? Best regards, Vassie Vassie Ware Professor, Molecular Biology Lehigh University Bethlehem, PA vcw0@lehigh.edu 172Kb

Link to this post | posted 15 Sep, 2023 22:01
Tamarah_Adair	Has anyone studied the holins in AZ?

Link to this post | posted 03 Jun, 2023 16:04

Tamarah_Adair

In Lakshmi and other AK phages GeneMark is showing a potential frameshift arrow and coding potential that some students have looked at and hypothesized that there are 2 genes (starting at 31127 and then switching frames at a polyG sequence to end at 31589), and then a second gene at 31589-33757 that make up a primase/polymerase AND a helicase instead of the one larger orf 31127-33757 that combines these domains and is annotated as primase/polymerase/helicase with HHPred evidence. In some draft phages, this long orf (31127-33757 in Lakshmi) appears to have a short overlapping gene about 100bp from the start, representing this extra coding potential that MAY be the second half of the first gene, as hypothesized by these students. (They did some modeling that supports their ideas.) The paper the students have https://www.frontiersin.org/articles/10.3389/fgene.2012.00242/full indicates there could be GGGGG slippery sequence. However, without further evidence (as of June 2023), we are NOT calling these 2 genes or a frameshift at this time, and instead calling the single long orf. Debbie added GeneMark output to illustrate. Agreed that something like what is described could be some sort of frameshift BUT an area of low coding potential that just happens to be higher CP in another frame is not unheard of. Only 1 ORF to call here. Bench data would be required here. Edited 06 Jun, 2023 01:52 185Kb

Link to this post | posted 03 Jun, 2023 16:03

Tamarah_Adair

In Lakshmi and other AK phages GeneMark is showing a potential frameshift arrow and coding potential that some students have looked at and hypothesized that there are 2 genes (starting at 31127 and then switching frames at a polyG sequence to end at 31589), and then a second gene at 31589-33757 that make up a primase/polymerase AND a helicase instead of the one larger orf 31127-33757 that combines these domains and is annotated as primase/polymerase/helicase with HHPred evidence. In some draft phages, this long orf (31127-33757 in Lakshmi) appears to have a short overlapping gene about 100bp from the start, representing this extra coding potential that MAY be the second half of the first gene, as hypothesized by these students. (They did some modeling that supports their ideas.) The paper the students have https://www.frontiersin.org/articles/10.3389/fgene.2012.00242/full indicates there could be GGGGG slippery sequence. However, without further evidence (as of June 2023), we are NOT calling these 2 genes or a frameshift at this time, and instead calling the single long orf.

Link to this post | posted 12 Sep, 2022 23:29
Tamarah_Adair	Job openings in the Department of Biology at Baylor University

Link to this post | posted 30 Jul, 2022 17:36
Tamarah_Adair	Hi. I have been using Arthrobacter hosts for several years and I am thinking about trying out hunting for Corynebacteriophage this year. Are there any suggestions for hosts or protocols? Thank you for any information. Tammy

Link to this post | posted 21 May, 2022 13:28
Tamarah_Adair	I was checking my Review to Improve on Casserole and there are changes to gpXX for each hypothetical protein. Is this an update?