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Recent Activity
All posts created by jbraverm
| Link to this post | posted 25 Mar, 2020 23:49 | |
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Why isn’t there a Pham report for a Pham that seems very common in the databases? Here is an example: Magic8 gene 92 Nothing behind the pham link - no PDF - I think that means it’s not on http://phages.wustl.edu/starterator/ . Yet, many BLAST hits for this gene/protein! Wouldn't a frequently found protein be assigned a Pham and have a starterator analysis done? Thanks. John |
Posted in: PECAAN → Could this Pham be improperly assigned in PECAAN?
| Link to this post | posted 25 Mar, 2020 23:49 | |
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Why isn’t there a Pham report for a Pham that seems very common in the databases? Here is an example: Magic8 gene 92 Nothing behind the pham link - no PDF - I think that means it’s not on http://phages.wustl.edu/starterator/ . Yet, many BLAST hits for this gene/protein! Wouldn't a frequently found protein be assigned a Pham and have a starterator analysis done? Thanks. John |
Posted in: PECAAN → Could this Pham be improperly assigned in PECAAN?
| Link to this post | posted 17 Feb, 2020 12:36 | |
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Thank you so much. Yes, that is what I wanted to know. I don't see that explanation anywhere else on the Bioinformatics Guide. The old format is here: https://seaphagesbioinformatics.helpdocsonline.com/article-37 Also, there is this instruction: https://seaphagesbioinformatics.helpdocsonline.com/officialdocumentation Results of the Starterator analysis. If the start is conserved throughout the members of the pham and yields the longest genes, write SS for “suggested start.” If it is not applicable, (orpham, only one possible start choice, etc) record NA. If it was run and was not informative (for example, the full length nucleotide sequences of the pham members are identical and all starts are present in all pham members, or pham members are too diverse and no real consensus is reached), write NI. Which I think maybe could add the point about MA where it mentions "conserved throughout"… that would be "conserved throughout MOST"? The "longest genes part," I am not sure about. |
Posted in: Starterator → Starterator Documentation
| Link to this post | posted 13 Feb, 2020 02:25 | |
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I am looking for a document that explains this: In the PDF for Pham 96380 at http://phages.wustl.edu/starterator/ Gene: Magic8_Draft_1 Start: 1, Stop: 567, Start Num: 23 Candidate Starts for Magic8_Draft_1: (Start: 23 @1 has 190 MA's), (Start: 25 @10 has 5 MA's), (31, 70), (32, 73), (68, 280), (72, 331), (81, 460), (98, 535), (102, 547), (106, 559), This is all the documentation I can find on the Bioinformatics Guide: https://seaphagesbioinformatics.helpdocsonline.com/article-23 And the material on the PDF seems out of date: "Annotation and bioinformatic analysis of bacteriophage genomes - user guide to DNA master" dated 2017 - now I cannot locate the PDF on-line. |
Posted in: Starterator → Starterator Documentation