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Recent Activity
Tutorial on Phamerator and Starterator Use?
| Link to this post | posted 28 Jan, 2016 20:21 | |
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Are there tutorials available for these two softwares? Those for DM are excellent for helping students (and new faculty) walk through issues that come up. If there are video or text tutorials available for the software inside the VM that would be really wonderful? Show me the way! (I'm almost certain they are out there. So please help me find them!) Thanks. |
| Link to this post | posted 29 Jan, 2016 17:37 | |
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We have something strange going on when we compare our auto-annotated Blast file in DNA master to what's in phamerator and starterator for ShiaLaBeouf_Draft. The gene product numbers/features don't align like they do for other phage genomes. Is this because of a difference in when we did our Blasting? The files aren't corrupt (the genome size is consistent with what we started with and what is reported on phagesdb). But, gp 42 is not the same… This might be a naive newbie confusion, but… help? |
| Link to this post | posted 29 Jan, 2016 20:01 | |
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joyous726 It is probably because the auto-annotations came up with different results (yours compared to the one done for the phamerator file). Each time an auto-annotation is run there is a potential for a different result (just one additional gene call or non-call can throw off all the numbers). That is one of the reasons you always want your students to refer to genes by coordinates and not by gp#. |
| Link to this post | posted 30 Jan, 2016 16:11 | |
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Lee HughesWe have the same issue - our genes are off by one number in Starterator reports. Not a big deal as long as students pay attention to start and stop co-ordinatesjoyous726 |
| Link to this post | posted 30 Jan, 2016 16:17 | |
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GregFrederick@letu.edu We have been listening back to the live stream from our training week - it is an excellent resource for jogging the memory: On the 12 / 8 stream at ~ 4hr:45 minutes Welkin introduces Starterator. I think that Steve talks about Phamerator on the same day but we have not gotten that far yet!! Also - http://phagesdb.org/media/docs/Starterator_Guide_2014_2.pdf |
| Link to this post | posted 01 Feb, 2016 21:15 | |
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Can you "overwhelm" Starterator? Analyzing one of our genes produced 351 tracks! The graph was incomplete: it only listed the first few start sites for just one of the tracks. The report appears to be useful, although it would be nice to see the graph. Thanks. |
| Link to this post | posted 01 Feb, 2016 21:40 | |
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fogartym1 The guide is useful. Thanks. I think this was the day I was sick in the morning and I apparently missed a lot. Can you help me find the link to the "live stream". I'm not finding it as I scan SEAPhages.org pages. Thanks in advance. Greg |
| Link to this post | posted 01 Feb, 2016 22:03 | |
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GregFrederick@letu.edufogartym1 Hi Greg: It is on this page from the workshop http://seaphages.org/meetings/10/ It reads view the live stream here … This is the direct link http://mediasiteex.hhmi.org/Mediasite/Catalog/Full/672215ce45df45caa93499b86d49c64821 |
| Link to this post | posted 01 Feb, 2016 22:15 | |
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fogartym1GregFrederick@letu.edufogartym1 Excellent!!!! Thanks! |
| Link to this post | posted 03 Feb, 2016 14:48 | |
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saleadon Hey Steve, What was the gene and Pham number that this happened on? –Dan |