SEA-PHAGES | All posts created by hkotturi

Link to this post \| posted 25 Apr, 2022 19:45
hkotturi	ball.1766 How should we label this? It looks like most have called it as "capsid and capsid maturation protease"…would you like us to continue using that notation? We are working with Cluster AU phage ScienceWizSam and AreFloNak. They both seem like they have this fusion protein. Other close matches are calling it capsid and capsid maturation proteases. Are we still following this format?

Posted in: Cluster AU Annotation Tips → capsid fusion

Link to this post \| posted 22 May, 2019 16:45
hkotturi	We are working with phage Fulbright and cannot access Starterator reports for the following genes. None of them are orphams. Starterator report 55791 report not found for Gene 43 Fulbright https://phagesdb.org/phams/55791/ Starterator report 55563 report not found for Gene 51 Fulbright https://phagesdb.org/phams/55563/ Starterator report 55854 report not found for Gene 59 Fulbright https://phagesdb.org/phams/55854/ Starterator report 55837 report not found for Gene 65 Fulbright https://phagesdb.org/phams/55837/ Starterator report 55152 report not found for Gene 72 Fulbright https://phagesdb.org/phams/55152/

Link to this post | posted 22 May, 2019 16:45

hkotturi

We are working with phage Fulbright and cannot access Starterator reports for the following genes. None of them are orphams.

Starterator report 55791 report not found for Gene 43 Fulbright
https://phagesdb.org/phams/55791/
Starterator report 55563 report not found for Gene 51 Fulbright
https://phagesdb.org/phams/55563/
Starterator report 55854 report not found for Gene 59 Fulbright
https://phagesdb.org/phams/55854/
Starterator report 55837 report not found for Gene 65 Fulbright
https://phagesdb.org/phams/55837/
Starterator report 55152 report not found for Gene 72 Fulbright
https://phagesdb.org/phams/55152/

Posted in: Starterator → Pham not found in Starterator

Link to this post \| posted 13 Mar, 2019 16:44
hkotturi	Hi, Just wanted to confirm this to see if I am on the right track. I have a student practicing annotation with Miaurora genome. It has already been annotated and submitted to GenBank. Miaurora has a frameshift in tail assembly chaperone (gene 10 and 11). My student is practicing documenting frameshifts. We generated a phamerator map with few close phage genomes (see attached image). So, if he were to work with HarperAnne_draft he would have to "add a gene" as gene 11 (with start and stop coordinates that would include Gene 10 Start and end with frameshift Stop). He would have to "add a gene" autoannotation in DNAMaster did not catch that extra part as shown in Owen_draft genome (gene 11). if he were to work with Owen_draft genome, he would follow the process described in the online guide (https://seaphagesbioinformatics.helpdocsonline.com/article-54) and just extend the start site for gene 11 as described on the webpage. am I right? Please let me know. 107Kb

Link to this post | posted 13 Mar, 2019 16:44

hkotturi

Hi,
Just wanted to confirm this to see if I am on the right track. I have a student practicing annotation with Miaurora genome. It has already been annotated and submitted to GenBank. Miaurora has a frameshift in tail assembly chaperone (gene 10 and 11). My student is practicing documenting frameshifts. We generated a phamerator map with few close phage genomes (see attached image).

So, if he were to work with HarperAnne_draft he would have to "add a gene" as gene 11 (with start and stop coordinates that would include Gene 10 Start and end with frameshift Stop). He would have to "add a gene" autoannotation in DNAMaster did not catch that extra part as shown in Owen_draft genome (gene 11).

if he were to work with Owen_draft genome, he would follow the process described in the online guide (https://seaphagesbioinformatics.helpdocsonline.com/article-54) and just extend the start site for gene 11 as described on the webpage.

am I right?

Please let me know.

Posted in: Annotation → Annotations of Microbacterium foliorum

Link to this post \| posted 21 Jan, 2017 20:05
hkotturi	Question - I was trying to learn using Phamerator software. I have downloaded the VirtualBox. Everything went well without any problems on my machine. But, When I try to start Phamerator, I get a message saying “”Database Setup Required.” “Phamerator needs to set up your database. Please enter your root database password.” I tried passwords for student access, faculty access and admin access none of them work. Do you know whats is going on? Can anyone help?

Link to this post | posted 21 Jan, 2017 20:05

hkotturi

Question - I was trying to learn using Phamerator software. I have downloaded the VirtualBox. Everything went well without any problems on my machine. But, When I try to start Phamerator, I get a message saying “”Database Setup Required.” “Phamerator needs to set up your database. Please enter your root database password.”

I tried passwords for student access, faculty access and admin access none of them work. Do you know whats is going on? Can anyone help?

Posted in: Phamerator → Install Guest Additions to VM ---- Without "SEAFaculty Login ability"

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