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Recent Activity
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
RyanWheeler posted in Plaques appear on spot test, don't appear in titer
All posts created by jawsWPI
Link to this post | posted 04 Feb, 2022 20:16 | |
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A new function has been added to the official function list: Phosphoribosyl transferase. Example genes are Phelipe_64 and Bosnia_40. Do not confuse with the phosphoribosyl pyrophosphate transferase function–these are two different enzymes in the nucleotide synthesis pathway. Evidence and rational can be found in the attached document. |
Link to this post | posted 13 Jan, 2022 19:20 | |
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For those who use PECAAN. Attached is the notes template (excel file) that my students will be using, and the instruction document. In the first round each student will annotate an assigned coordinate range. In the second round they will peer review (as Kristen's students do) a different range with access to the first round notes. |
Link to this post | posted 18 Jun, 2020 14:57 | |
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I would agree that the two smaller ones should be NKF but, the 1200bp is probably a minor tail. An HHPred run analysis of the 1200bp protein should give good hits to collagen-like or glycine-rich proteins if it is a minor tail. The gene count in your A3 may be off because gene 1 (HNH endonuclease) is often not included in the auto-annotation and has to be added manually. |
Link to this post | posted 02 Jun, 2020 16:49 | |
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QCing Chivey, and it looks like we are perpetuating another bad minor tail protein call in the EF phages. Pham 38688, found in several different clusters, is a small protein (350 -400 bp) well upstream of the tapemeasure protein in EF (around gp22); a significant majority of the pham members assign NKF. Best HHPred hit (see attached) in all non-draft EF is from pfam (phage HK97-gp10) 'putative tail-component' (TIGRFAMs calls this same gene a model for an uncharacterized, highly divergent bacteriophage family); no good PDB or collagen or coiled-coiled domains. Based on this and the May 27 SMART conversation I'm changing Chivey's to NKF–heads-up for other EF. |
Link to this post | posted 05 Feb, 2020 15:40 | |
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Hi Jamie, Are you using the dropdown function choice menu in PECAAN? My students couldn't get a green check mark unless they type in an exact match to the functions in PECAAN, or actually selected an existing function from the dropdown menu. And of choice clicking 'save' BEFORE leaving the page. |
Link to this post | posted 28 Jan, 2020 17:30 | |
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How long does it take PECAAN to update pham numbers for the Starterator and phageDB links? We are annotating on PECAAN, and over the past 2 days have run into several instances where these links gave the following error message: "Page/Report not found Error 404" for a gene that isn't an orpham. The stand-alone phamerator map pham numbers are accurate (embedded PECAAN pham map numbers are not), and can be used on phagesDB or the stand-along starterator site to get information. So, it looks like this is a PECAAN update issue. |
Link to this post | posted 06 Jun, 2019 12:51 | |
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How hard and fast is the minor tail protein size range (1-3kb)? I'm reviewing an A1 annotation that has assigned the 'minor tail protein' function to 333bp, 348 bp and 447 bp ORF's, mostly based (I think) on a FEW cases in each pham that have given this functional assignment to similarly (small) sized ORFs. I want to change these all to NKF, first based on size and second based on total number of minor tails of the correct size and position. |
Link to this post | posted 10 Apr, 2019 19:05 | |
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Thanks Chris. That worked and I could see the changes during each iteration.![]() |
Link to this post | posted 10 Apr, 2019 15:27 | |
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Lee Hughes This was also my thought and I have done everything I can think of to make sure the fields are truly empty before using the DNA master tools to transfer copy data from one field to another. The hidden space or hard return appears to be imbedded in the PECAAN text file that I'm copying into DNA master documentation before parsing. Here is the only hint I have: the last gene product, which is NKF, actually is labeled as hypothetical. I've looked at the text file (copied below) and the only difference is that there isn't a "CDS" immediately after the double quotes (signifying the start of the next feature call) for this last gene. Attached is what the text file looks like in notepad, but below is what I got when I copied the highlighted section and pasted that text into this message. There definitely seems to be a carriage return right after every note except the last one. CDS 54801 - 55664 /gene="81" /product="gp81" /locus tag="NarutoRun_81" /note="" CDS 55666 - 56145 /gene="82" /product="gp82" /locus tag="NarutoRun_82" /note="" Claire is this something new that we have to work around (this is the first time I have used PECANN for the full annotations)? I assume there haven't been issues before when parsing PECAAN CDS functions text files. |
Link to this post | posted 09 Apr, 2019 19:22 | |
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Claire Rinehart I'm trying to generate a DNA master minimal file using copy/paste/parse from an exported CDS function, but it won't auto-label the blank products as "hypothetical" it's just leaving them blank. I tried using the 'new SEA format' full annotation, but that puts NKF in the function field which also causes the same problem if you follow the entire step sequence for generating a minimal file from the guide (from the guide: "NKF" is also not considered default, and won't be overwritten" ![]() Is anyone else having this problem? Is there a solution besides pasting in "hypothetical" in to all the blank product fields? |