SEA-PHAGES | All posts created by ball.1766

Link to this post \| posted 10 Jan, 2020 17:45
ball.1766	Just a heads up…it appears that the WINE option is not compatible with the newest Mac OS (Catalina). We had several students attempt to run DnaMaster through WINE and the only difference we could see between those who were successful and those who were not was in which operating system they were running. We have those students attempting to follow the virtual machine instructions so I am hopeful we will still get everyone up and running but I wanted to provide a warning for those who have not started the semester yet so they can be prepared.

Link to this post | posted 10 Jan, 2020 17:45

Just a heads up…it appears that the WINE option is not compatible with the newest Mac OS (Catalina). We had several students attempt to run DnaMaster through WINE and the only difference we could see between those who were successful and those who were not was in which operating system they were running. We have those students attempting to follow the virtual machine instructions so I am hopeful we will still get everyone up and running but I wanted to provide a warning for those who have not started the semester yet so they can be prepared.

Posted in: Using WINE to run DNA Master on a Mac → Help with WINE

Link to this post \| posted 05 Jul, 2018 02:35
ball.1766	While QC'ing Zerg I came across an ORF where other Pham members have been called as MPME1 and 2 (or just MPME protein) but many other members of the pham didn't call a function at all so I am not sure how to proceed. I have included the alignment with Fruitloop 71 but since it is not an identical match I don't know if I should call it MPME2 or if it is a new one (or nothing at all). Score Expect Method Identities Positives Gaps 163 bits(412) 8e-50 Compositional matrix adjust. 74/110(67%) 85/110(77%) 0/110(0%) Query 14 MPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEASTFALIPTKHYGPF 73 M + G+D+ HLS EHRDRAWRDRFNARWH+DYGGWIRTRPQD+ASTFALIP + YGPF Sbjct 1 MKASTQGTDIPHLSSEHRDRAWRDRFNARWHHDYGGWIRTRPQDDASTFALIPDERYGPF 60 Query 74 TEDHSCPACLVVHPPEDCPVLSGNTDMLVVFDYDTSPNKAQADTADDDPR 123 EDHSCP CL +H P++CPVLS + DYDT+P QADTA DD R Sbjct 61 VEDHSCPYCLAIHQPQECPVLSRYAGRAIASDYDTTPKNTQADTAADDLR 110 Edited 05 Jul, 2018 13:01

Link to this post | posted 05 Jul, 2018 02:35

ball.1766

While QC'ing Zerg I came across an ORF where other Pham members have been called as MPME1 and 2 (or just MPME protein) but many other members of the pham didn't call a function at all so I am not sure how to proceed. I have included the alignment with Fruitloop 71 but since it is not an identical match I don't know if I should call it MPME2 or if it is a new one (or nothing at all).

Score	Expect	Method	Identities	Positives	Gaps
163 bits(412)	8e-50	Compositional matrix adjust.	74/110(67%)	85/110(77%)	0/110(0%)
Query  14   MPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEASTFALIPTKHYGPF  73
            M  +  G+D+ HLS EHRDRAWRDRFNARWH+DYGGWIRTRPQD+ASTFALIP + YGPF
Sbjct  1    MKASTQGTDIPHLSSEHRDRAWRDRFNARWHHDYGGWIRTRPQDDASTFALIPDERYGPF  60

Query  74   TEDHSCPACLVVHPPEDCPVLSGNTDMLVVFDYDTSPNKAQADTADDDPR  123
             EDHSCP CL +H P++CPVLS      +  DYDT+P   QADTA DD R
Sbjct  61   VEDHSCPYCLAIHQPQECPVLSRYAGRAIASDYDTTPKNTQADTAADDLR  110

Edited 05 Jul, 2018 13:01

Posted in: Cluster F Annotation Tips → MPMEs--which one?

Link to this post \| posted 02 May, 2018 02:40
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?

Posted in: Cluster AU Annotation Tips → capsid fusion

Link to this post \| posted 18 Dec, 2017 18:12
ball.1766	It looks like each gene gets a strong conserved domain hit in BLASTp (see attached screen shot). So should I list the functions as "lysin A, peptidase domain" and "lysin A, amidase domain"? 84Kb

Posted in: Gene or not a Gene → Lysin A split in 2 or sequencing error-B1 cluster

Link to this post \| posted 14 Dec, 2017 17:03
ball.1766	I have come across an anomaly while trying to wrap up the annotation QC of a B1 phage, Phergie. gp47 and gp48 both have BLAST hits to LysA. When comparing this area to other very similar phage, there is one longer ORF in this position that is called as LysA. There is strong coding potential for both ORFs but the reading frame shifts. I do not know enough about sequencing and finishing genomes to tell if this is just an error (which is my initial thought) or something more interesting. Thoughts? 75Kb

Link to this post | posted 14 Dec, 2017 17:03

ball.1766

I have come across an anomaly while trying to wrap up the annotation QC of a B1 phage, Phergie. gp47 and gp48 both have BLAST hits to LysA. When comparing this area to other very similar phage, there is one longer ORF in this position that is called as LysA. There is strong coding potential for both ORFs but the reading frame shifts. I do not know enough about sequencing and finishing genomes to tell if this is just an error (which is my initial thought) or something more interesting.

Thoughts?

Posted in: Gene or not a Gene → Lysin A split in 2 or sequencing error-B1 cluster

Link to this post \| posted 28 Jan, 2017 20:45
ball.1766	Most of our students this year are using Macs so they are trying to run DNA Master using WINE but we are running into issues. None of them seem to be able to run the auto-annotation or BLAST genes (individual or batch) and a few of them cannot even open a .dnam5 file that I provided as a work around (I ran the auto-annotation and BLAST and just distributed the file). Any suggestions? I'm a PC person so I don't have the slightest idea of where to start troubleshooting.

Link to this post | posted 28 Jan, 2017 20:45

ball.1766

Most of our students this year are using Macs so they are trying to run DNA Master using WINE but we are running into issues. None of them seem to be able to run the auto-annotation or BLAST genes (individual or batch) and a few of them cannot even open a .dnam5 file that I provided as a work around (I ran the auto-annotation and BLAST and just distributed the file). Any suggestions? I'm a PC person so I don't have the slightest idea of where to start troubleshooting.

Posted in: DNA Master → Running DNA Master on a Mac using Wine

Link to this post \| posted 23 Mar, 2016 18:12
ball.1766	I have a student who has Linux on his home computer and would like to download Phamerator. Could you please send me the appropriate file/password that he would need to be able to get it up and running? Thanks, Sarah

Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM

Link to this post \| posted 11 Mar, 2016 18:07
ball.1766	TyrionL crashes on the very first pham (Pham 1029) every time I try to run it. I've tried it as TyrionL and as TyrionL_Draft, both with the same outcome. Any help would be appreciated!

Posted in: Starterator → phage that crash starterator

Link to this post \| posted 09 Feb, 2016 17:50
ball.1766	I have tried all of the suggested fixes (checking the database, deleting intermediate files) but Starterator still crashes on Pham 11430 of WillSterrel_Draft every time I try to run it. Any suggestions would be appreciated since we start annotating it next week.

Posted in: Starterator → phage that crash starterator

Link to this post \| posted 09 Feb, 2016 17:47
ball.1766	I have tried all of the suggested fixes (checking the database, deleting intermediate files) but Starterator still crashes on Pham 11430 of WillSterrel_Draft every time I try to run it. Any suggestions would be appreciated since we start annotating it next week.

Posted in: Starterator → Read First: Common Starterator Troubleshooting

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