SEA-PHAGES | All posts created by cdherren

Link to this post \| posted 25 Jan, 2021 02:37
cdherren	I'm having the same issue on 2 different PCs during off peak hours. I'm not getting a single return after an overnight run.

Posted in: DNA Master → DNAMaster BLAST failure

Link to this post \| posted 21 Mar, 2019 15:55
cdherren	PECAAN only allows Y-int or S-int integrase choices. Are they both Y-int?

Posted in: Cluster CY Annotation Tips → two integrases

Link to this post \| posted 21 Mar, 2019 15:13
cdherren	We also have a Fic/DOC family hit in EnalisNailo_33. It's being annotated by others as NKF, helix turn helix DNA binding domain, DNA binding protein, DNA primase/helicase, and capsid maturation protease. The only non-phage hits are Fic/DOC in HHPred and a really low hit in CDD. Our's is 100% prob., 85.5% coverage, e-36 in HHPred. Kiko_36 ultimately went with NKF, but pollux submitted to NCBI as helix-turn-helix DNA binding domain protein. Is there a consensus on the function? I'm leaning towards NKF right now. 26Kb

Link to this post | posted 21 Mar, 2019 15:13

cdherren

We also have a Fic/DOC family hit in EnalisNailo_33.

It's being annotated by others as NKF, helix turn helix DNA binding domain, DNA binding protein, DNA primase/helicase, and capsid maturation protease.

The only non-phage hits are Fic/DOC in HHPred and a really low hit in CDD. Our's is 100% prob., 85.5% coverage, e-36 in HHPred.

Kiko_36 ultimately went with NKF, but pollux submitted to NCBI as helix-turn-helix DNA binding domain protein. Is there a consensus on the function? I'm leaning towards NKF right now.

Posted in: Functional Annotation → FIC family protein

Link to this post \| posted 24 Jan, 2018 21:02
cdherren	I still like the inclusive 1 file for an entire phage. Will that ever be an option on the phagesdb site? We group annotate and use 1 copy of a complete Starterator and GeneMark report for working in class. It's also helpful because we hand annotate every ORF on paper and keep a binder for each phage with a cover page, Starterator report, GeneMark reports, tRNA search results, and a single form fill page for each gene we annotate, add, delete, modify, etc. for our permanent records. I generally run Starterator myself and then just provide the pdf for the class, so I would like to update the VM and Starterator on my Mac.

Link to this post | posted 24 Jan, 2018 21:02

cdherren

I still like the inclusive 1 file for an entire phage. Will that ever be an option on the phagesdb site?

We group annotate and use 1 copy of a complete Starterator and GeneMark report for working in class. It's also helpful because we hand annotate every ORF on paper and keep a binder for each phage with a cover page, Starterator report, GeneMark reports, tRNA search results, and a single form fill page for each gene we annotate, add, delete, modify, etc. for our permanent records.

I generally run Starterator myself and then just provide the pdf for the class, so I would like to update the VM and Starterator on my Mac.

Posted in: Starterator → Read First: Common Starterator Troubleshooting

Link to this post \| posted 24 Jan, 2018 19:39
cdherren	Is Starterator in Ubuntu running? I've been trying to run a report for Pollywog_Draft for several days now and it starts, but never makes any progress. I've cleared out the Intermediate Files folder and upped the virtual memory to 2024M.

Posted in: Starterator → Read First: Common Starterator Troubleshooting

Link to this post \| posted 14 Feb, 2017 16:01
cdherren	tRNAscan-SE 2.0 has moved again: http://lowelab.ucsc.edu/tRNAscan-SE/

Posted in: tRNAs → tRNAscan-SE site has changed?

Link to this post \| posted 10 Feb, 2017 17:57
cdherren	Perfect. Thanks!

Posted in: tRNAs → tRNAscan-SE site has changed?

Link to this post \| posted 09 Feb, 2017 16:08
cdherren	Has tRNA-scan-SE been changed? It now directs to: https://galaxy.pasteur.fr/forms::trnascan and none of the advanced functions detailed in the Annotation Guide apply (pp. 97-100)

Posted in: tRNAs → tRNAscan-SE site has changed?

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