SEA-PHAGES | All posts created by beckiebortz

Link to this post \| posted 12 Nov, 2017 15:56
beckiebortz	Kiko_draft_36 BLAST data (attached) shows strong hits to FIC family protein in many bacteria. HHpred also hits FIC protein/domain as well as many other things (attached). What do you think is the appropriate functional call? I have also attached the product sequence if you want to take it to HHpred yourself to see the full data. Edited 12 Nov, 2017 15:57 480Kb 240Kb 11Kb

Posted in: Functional Annotation → FIC family protein

Link to this post \| posted 07 Nov, 2017 19:48
beckiebortz	I am currently having this same issue. I have tried to rebuild with the directions for "How to fix a corrupt DNA Master file" and there were some files missing and subsequently replaced. However, I am getting the same error messages post rebuild. I was also trying to create a profile and got the message "No ORFs have been parsed from this documentation". I tried parsing the documentation but got this third error message "Index is out of date. Index: FeatureID". Note: I was able to copy the documentation to a Word document. What do you think my next step should be?

Link to this post | posted 07 Nov, 2017 19:48

beckiebortz

I am currently having this same issue. I have tried to rebuild with the directions for "How to fix a corrupt DNA Master file" and there were some files missing and subsequently replaced. However, I am getting the same error messages post rebuild. I was also trying to create a profile and got the message "No ORFs have been parsed from this documentation". I tried parsing the documentation but got this third error message "Index is out of date. Index: FeatureID". Note: I was able to copy the documentation to a Word document. What do you think my next step should be?

Posted in: DNA Master → TbRegions: Cannot perform this operation on a closed dataset

Link to this post \| posted 01 Mar, 2017 17:16
beckiebortz	This question concerns a Gordonia phage and all other phages in its cluster are draft. Essentially there is a forward gene that has good coding potential among a group of reverse genes. My students are inclined to call the forward gene but there is confusing evidence. There is a reverse gene called by Glimmer-only in the same region as the forward gene and the confusion is somewhat compounded by gene numbers that differ in DNA master and Phamerator. Our decision at this point is to delete the reverse Gene 42/43 (29120-29410) and perhaps make adjustments to the starts of the earlier reverse gene (28972-29163R) and the forward gene (29243-29386) based on BLAST hits. The later reverse gene should remain as auto-annotated. Does this seem like a legitimate call or have we missed some critical piece of evidence? Edited 01 Mar, 2017 17:45 116Kb 191Kb 102Kb

Link to this post | posted 01 Mar, 2017 17:16

beckiebortz

This question concerns a Gordonia phage and all other phages in its cluster are draft. Essentially there is a forward gene that has good coding potential among a group of reverse genes. My students are inclined to call the forward gene but there is confusing evidence. There is a reverse gene called by Glimmer-only in the same region as the forward gene and the confusion is somewhat compounded by gene numbers that differ in DNA master and Phamerator. Our decision at this point is to delete the reverse Gene 42/43 (29120-29410) and perhaps make adjustments to the starts of the earlier reverse gene (28972-29163R) and the forward gene (29243-29386) based on BLAST hits. The later reverse gene should remain as auto-annotated. Does this seem like a legitimate call or have we missed some critical piece of evidence?

Edited 01 Mar, 2017 17:45

Posted in: Gene or not a Gene → Forward gene with good evidence among reverse genes

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