Link to this post | posted 01 Dec, 2025 17:25
bburnes	Thank you so much!

Link to this post | posted 21 Oct, 2025 20:47
bburnes	Hi Chris, Would you be able to run cluster FC phage Phrampa? Thanks! Brian

Link to this post | posted 21 Oct, 2025 20:46
bburnes	Ohhhh yes, you told us that in the workshop. Thanks for your patience!

Link to this post | posted 21 Oct, 2025 17:26
bburnes	Hi, Cluster FC phage Phrampa shows 292 auto-annotated genes in PECAAN and the PECAAN Pham map, but the Phamerator website shows 322 genes. There appears to be genome duplication from gene 286 to the end. How should we proceed? Thanks. Brian

Link to this post | posted 03 Oct, 2025 17:42
bburnes	Thanks, that is a good point to keep in mind. I appreciate your comment.

Link to this post | posted 02 Oct, 2025 16:17
bburnes	Thanks!

Link to this post | posted 01 Oct, 2025 20:17

bburnes

Hi all, Our class is looking at Gene 1 (stop 685), which is called by glimmer and genemark (Both), the gene is long enough (120 nt = 40aa), has good coding potential (Yes), has SYNTENY (Yes with FC phages MIMI, TALIA, and ATUIN), is the only gene in the region (Yes), and has a function predicted, (Hypothetical Protein). We need help choosing a start. Both starts 1 and 10 are called by Glimmer and GeneMark. In STARTERATOR, start 1 has two MA's while start 10 has six MA's. Start 1 has lower RBS scores (Z-score of 1.399 and a final score of -6.961), and start 10 has a z-score of 2.024 and a final score of -4.608. Start 1 also has the longest open reading frame. Start 1 gives us 1:1 matches to the highest GenBank hit, while Start 10 gives us 1:1 matches to the second and third GenBank hits. Basically, the highest RBS scores go with start 10, but the longest open reading frame and the top hits go with start 1. Which would be a better start? Thanks!