SEA-PHAGES | All posts created by andrea

Link to this post \| posted 16 Apr, 2021 16:39
andrea	Hello everyone, I’d welcome some thoughts on our JalFarm20_3 start site. Thank you! Please see attached for screen shots. 1. Glimmer and GeneMark agree on start: nucleotide 797. Not longest ORF. Could be nucleotide 671 or 659, but that would create overlap with JalFarm20_3 by 28 or 40 bp. 2. The start is not conserved among all members of the pham (Starterator). JalFarm20_3 start is 152, same as UncleRicky_3, UPitt annotation-sequenced in 2017; most called is 103; similar phages earlier start 93 (e.g. SpikeLee_3; Bobi_3). 3. Currently predicted start site does not include all coding potential in GeneMark in +2 frame. 4. For genes with functional predictions, start bp 797 includes the full-length protein using BLASTP, terminase large subunit. BLASTP with start bp 671 (overlaps with JalFarm20_2: by 28 bp) produces alignments as well. 5. Start bp 671 has a better final RBS score. 6. Synteny evident. 596Kb

Link to this post | posted 16 Apr, 2021 16:39

Hello everyone,

I’d welcome some thoughts on our JalFarm20_3 start site. Thank you! Please see attached for screen shots.

1. Glimmer and GeneMark agree on start: nucleotide 797. Not longest ORF. Could be nucleotide 671 or 659, but that would create overlap with JalFarm20_3 by 28 or 40 bp.
2. The start is not conserved among all members of the pham (Starterator). JalFarm20_3 start is 152, same as UncleRicky_3, UPitt annotation-sequenced in 2017; most called is 103; similar phages earlier start 93 (e.g. SpikeLee_3; Bobi_3).
3. Currently predicted start site does not include all coding potential in GeneMark in +2 frame.
4. For genes with functional predictions, start bp 797 includes the full-length protein using BLASTP, terminase large subunit. BLASTP with start bp 671 (overlaps with JalFarm20_2: by 28 bp) produces alignments as well.
5. Start bp 671 has a better final RBS score.
6. Synteny evident.

Posted in: Choosing Start Sites → Second opinion Cluster F1 Gene Start Site

Link to this post \| posted 25 Apr, 2018 21:48
andrea	We have a question regarding Bones_45, an A1 cluster phage our class is annotating. One of our students noticed that the Pham number on Phamerator, 42083 (561 members) varies from the Pham number found in PhagesDB, 45161 (580 members). Pham 42083 is not found in PhagesDB. Both indicate the function as DNA Polymerase I. Any insight on the discrepancy would be appreciated.

Posted in: Web Phamerator → Pham Number Discrepancy

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