Link to this post | posted 11 May, 2018 12:42
Tamarah_Adair	When I BLAST 1 gene at a time, I get OLE 8040152. How do you limit the BLAST to a set of genes? Thanks.

Link to this post | posted 11 May, 2018 12:16

Tamarah_Adair

There are 103 genes for Sonali. When we BLAST we receive 20 results and the rest of the genes return "There are no BLAST results for this feature". The BLAST freezes before it finishes and we have tried it several times. The report that eventually populates has lines like the following. Is this a complete BLAST that just has very few hits? Why are the feature numbers greater than our feature list? Thanks! Sent 25 requests (25 total) to the QBlast server. Checking for completed results at 9:33:06 PM… Error (12) retrieving results for RID FA02Z622015 for feature 110 Error (12) retrieving results for RID FA034F2E015 for feature 112 Error (12) retrieving results for RID FA03AAG9014 for feature 115 Error (12) retrieving results for RID FA03FMB7014 for feature 116 Error (12) retrieving results for RID FA03MXTY015 for feature 125 Error (12) retrieving results for RID FA03VVRG015 for feature 126 Error (12) retrieving results for RID FA0409U7015 for feature 127 Error (12) retrieving results for RID FA045PJ8014 for feature 128 Error (12) retrieving results for RID FA04BUFP014 for feature 129 Error (12) retrieving results for RID FA04GD2D014 for feature 130 Error (12) retrieving results for RID FA04NZ27014 for feature 131 Error (12) retrieving results for RID FA04VYNG014 for feature 132 Error (12) retrieving results for RID FA050CWU015 for feature 133 Error (12) retrieving results for RID FA0551M0015 for feature 134 Error (12) retrieving results for RID FA05B09Z015 for feature 135 Error (12) retrieving results for RID FA05GD74015 for feature 136 Error (12) retrieving results for RID FA05P9X5014 for feature 137 Error (12) retrieving results for RID FA061R6R014 for feature 139 Error (12) retrieving results for RID FA06HHWZ014 for feature 142 Error (12) retrieving results for RID FA06PCEC014 for feature 143 20 results read; still waiting for 5 results… Continuing to send queries at 9:46:44 PM… Sent 25 requests (50 total) to the QBlast server. Checking for completed results at 9:48:53 PM… Error (12) retrieving results for RID FA10M2XR014 for feature 146 Error (12) retrieving results for RID FA10TKEV014 for feature 147 4.62Mb

Link to this post | posted 03 May, 2018 18:46

Tamarah_Adair

Hi. We have had our annotations returned because we did not realize there was a new annotation guide (sorry!) Would you mind looking at these examples annotations and answer a few questions before we upload our DNAMAster files. 1. We are annotating A. globiformis phages. There are not many annotated phages or known gene functions in these clusters, so starterator is Not Informative, correct? 2. Synteny is described in detail, but for phages in new clusters, which phage should be referenced, or should we just use the list order and not reference the genome? or say NKF? For example, terminase below? SSC: start: 1349bp, stop: 1984bp CP: Yes SCS: both ST: NI Blast-Start: Arthrobacter sp. TMN-18, gp: N/A NCBI, Q:25S:27 coverage: 0.92 E-value: 0 , Nandita_Draft, gp: 5 PhagesDB, Q:1S:1 coverage: n/a E-value: e-107 Gap: 4bp Overlap LO: NA, RBS: Kibbler7, Karlin Medium, Zscore: 2.23, Final Score: -4.085, No F: terminase, small subunit SIF-Blast: NKF SIF-HHPred: Phage terminase, small subunit [Mobilome: prophages, transposons]COGN/a gp: N/a accession number: COG3747 alignment: 0.132 probability: 99.65 SIF-Syn: NKF Notes: NCBI hit is bacterial/hypothetical, Nandita is a draft, so the only hit is a HHPRED hit to COG. 3. Is it a correct interpretation of the guide to put NKF for all SIF if the gene function is determined to be NKF, or do you want to see the hits that were used to come to that conclusion. For example, is this annotation acceptable for a gene of nkf? SSC: start: 8565bp, stop: 8840bp CP: Yes SCS: both ST: NI Blast-Start: Arthrobacter sp. EpRS71, gp: N/A NCBI, Q:3S:4 coverage: 96 E-value: 8.6E-38 , Nandita_Draft, gp: 14 PhagesDB, Q:1S:12 coverage: N/A E-value: 2E-30 Gap: 4bp Overlap LO: NA, Lorf had a 39 bp overlap with the previous gene RBS: Kibbler7, Karlin Medium, Zscore: 1.137, Final Score: -7.054, No F: NKF SIF-Blast: NKF SIF-HHPred: NKF SIF-Syn: NKF Notes: 4. How do we add an underscore in the locus tag for all the genes at once? Thank you!

Link to this post | posted 09 Apr, 2018 20:53
Tamarah_Adair	Does anyone have the genome sequence of Arthrobacter sp. ATCC 21022?

Link to this post | posted 25 Jan, 2018 01:59
Tamarah_Adair	I think there must have just been a glitch on Monday? Everything was working fine today. Thanks.

Link to this post | posted 23 Jan, 2018 15:03
Tamarah_Adair	Thanks. We will try again.

Link to this post | posted 23 Jan, 2018 02:39

Tamarah_Adair

Keith Hutchison Tamarah Adair Is the link on the http://cobamide2.bio.pitt.edu/computer.htm working? We are having difficulty today getting an updated version that will auto-annotate. We have tried the slip stream file and it still does not work. Last week we were not having this issue. Thanks! Tamarah, I had two students with a similar problem. In both cases when I had them check the version number it was 5.22.21 which is way out of date. In both cases they'd used the link on seaphages.org. In both cases if they deleted the installation and downloaded from the link on phagesdb.org it fixed the problem. Keith Both of these links take me to the same web page. Am I missing something?

Link to this post | posted 22 Jan, 2018 23:01
Tamarah_Adair	Is the link on the http://cobamide2.bio.pitt.edu/computer.htm working? We are having difficulty today getting an updated version that will auto-annotate. We have tried the slip stream file and it still does not work. Last week we were not having this issue. Thanks!

Link to this post | posted 17 Jan, 2018 16:30

Tamarah_Adair

We were having some problems with DNAMaster in Wine last week, but I think we have them resolved. After starting the program, use Help/Update to make sure you have the most recent build installed. Then File/Quit (Don't Quit Wine/ Quit DNAMaster.)Reopen DNA Master and check under About to see if you have the Dec2017 build. Then use the information in the attached pdf to make sure you fix the settings that have to do with the server settings. Make sure you Apply/OK/Save the settings. Then File/Quit again. These settings should work for auto-annotation. 166Kb

Link to this post | posted 17 Jan, 2018 14:21

Tamarah_Adair

We have been working on designing PCR primers specific for Arthobacter phage isolated on the ATCC 21022 host. We need samples of phage lysate and DNA from phages in clusters AM, AP, AR, AS, AT and AV. Is this a request that should go to the Univ of Pittsburg archive or should I reach out to individuals? The samples should be sent to Tamarah Adair Baylor University Dept of Biology 101 Bagby BSB Room B207 Waco, TX 76706 Thanks!