SEA-PHAGES | All posts created by kmaclea

Link to this post \| posted 31 Mar, 2020 02:43
kmaclea	Dan got in touch, thank you for that! He already worked his magic! Kyle – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Posted in: Annotation → Gene Numbering Questions and More: Phage SilentRX (UNK)

Link to this post \| posted 30 Mar, 2020 03:33
kmaclea	Thank you, Debbie! Great questions, and we definitely have not investigated yet. I will try to guide the students in thinking about them this week. (Made more "interesting" because we are all doing this remotely, not side-by-side like before!) Side question: We have another Phage that we sequenced at the same time as SilentRX in our DOGEMs pool that was complete. We have recently identified this sequence I've been calling Brother-of-SilentRX as Phage Gole. Given you guys are closed down right now, can we get our DOGEMs Contig 1 assigned as Gole, and then Phamerated at some point? I will also be doing a summer course on phage annotation and could do Gole at that point instead if that makes more sense time-wise based on all you guys are trying to handle at the moment. Thank you, sincerely! Kyle – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post | posted 30 Mar, 2020 03:33

kmaclea

Thank you, Debbie! Great questions, and we definitely have not investigated yet. I will try to guide the students in thinking about them this week. (Made more "interesting" because we are all doing this remotely, not side-by-side like before!)

Side question: We have another Phage that we sequenced at the same time as SilentRX in our DOGEMs pool that was complete. We have recently identified this sequence I've been calling Brother-of-SilentRX as Phage Gole. Given you guys are closed down right now, can we get our DOGEMs Contig 1 assigned as Gole, and then Phamerated at some point? I will also be doing a summer course on phage annotation and could do Gole at that point instead if that makes more sense time-wise based on all you guys are trying to handle at the moment.

Thank you, sincerely!

Kyle

–
Kyle MacLea
Associate Professor, University of New Hampshire at Manchester
kyle.maclea@unh.edu +1 603-641-4129

Posted in: Annotation → Gene Numbering Questions and More: Phage SilentRX (UNK)

Link to this post \| posted 30 Mar, 2020 02:06
kmaclea	Hi all, We are working on phage SilentRX, which is currently assigned to Unknown (UNK) cluster, with its closest relatives in cluster AP. Students are about to start in earnest on annotation and first-pass gene assignments have been given out, but I have some weirdness I didn't notice before. At first glance it looked like SilentRX had 99 genes. But now it appears not… Autoannotation in DNA Master finds 100 genes with default settings. Phagesdb and Phamerator at first glance appears to find 99 genes, but gene 94 is missing, so this looks like 98 genes. Because of the numbering differences, the gene numbers in DNA master and Phagesdb/Phamerator are not in agreement. I am working out what to do next with gene numbering system. Any suggestions? Other questions: 1. Why is Gene 94 missing? 2. I have the final gene doing weird things. Gene 100 (Auto annotation) appears to be a reverse gene that crosses from position 678 to 65131. Is this likely to be a real gene? The same gene in Phagesdb is called Gene 99. And weirdly enough it has a second gene member in its Pham–SilentRX Gene 98. So it predicts that Genes 98 and 99 (phages db) or presumably 99 and 100 (autoannotation) are members of the same Pham, with one of them crossing position zero. Is this likely to be real? Any thoughts or suggestions appreciated! – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post | posted 30 Mar, 2020 02:06

kmaclea

Hi all,

We are working on phage SilentRX, which is currently assigned to Unknown (UNK) cluster, with its closest relatives in cluster AP.

Students are about to start in earnest on annotation and first-pass gene assignments have been given out, but I have some weirdness I didn't notice before.

At first glance it looked like SilentRX had 99 genes. But now it appears not…

Autoannotation in DNA Master finds 100 genes with default settings.

Phagesdb and Phamerator at first glance appears to find 99 genes, but gene 94 is missing, so this looks like 98 genes.

Because of the numbering differences, the gene numbers in DNA master and Phagesdb/Phamerator are not in agreement.

I am working out what to do next with gene numbering system.

Any suggestions?

Other questions:
1. Why is Gene 94 missing?

2. I have the final gene doing weird things. Gene 100 (Auto annotation) appears to be a reverse gene that crosses from position 678 to 65131. Is this likely to be a real gene? The same gene in Phagesdb is called Gene 99. And weirdly enough it has a second gene member in its Pham–SilentRX Gene 98. So it predicts that Genes 98 and 99 (phages db) or presumably 99 and 100 (autoannotation) are members of the same Pham, with one of them crossing position zero. Is this likely to be real?

Any thoughts or suggestions appreciated!

–
Kyle MacLea
Associate Professor, University of New Hampshire at Manchester
kyle.maclea@unh.edu +1 603-641-4129

Posted in: Annotation → Gene Numbering Questions and More: Phage SilentRX (UNK)

Recent Activity

All posts created by kmaclea