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All posts created by cdherren
| Link to this post | posted 25 Jan, 2021 02:37 | |
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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 | |
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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 | |
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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. |
26KbPosted in: Functional Annotation → FIC family protein
| Link to this post | posted 24 Jan, 2018 21:02 | |
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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 19:39 | |
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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. |
| Link to this post | posted 14 Feb, 2017 16:01 | |
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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 | |
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Perfect. Thanks! |
Posted in: tRNAs → tRNAscan-SE site has changed?
| Link to this post | posted 09 Feb, 2017 16:08 | |
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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?