Link to this post | posted 09 May, 2019 13:46

fogartym1

There are some recent published genome additions to Genbank and phagesdb that are very relevant for my annotation of Sixama. However, when I hit the rerun button for phagesdb and NCBI in PECAAN it is not updating. If I change the start site it updates, but for most genes I don't want to change the start site. Is there a way to rerun the databases (ideally for the entire genome at once)? Thanks Marie

Link to this post | posted 24 May, 2018 02:05

fogartym1

Hi Welkin - This article is helpful, thank you. Based on this article, I would like to call Octobien14_gp36 as lysin A, N-acetyl-β-D-muramidase" - it has conserved domain pfam01510 as does phage BPs and BXZ1. It shows a 164 blast p score alignment (64 % query coverage) with lysin A of BPs. For Octobien_gp35, I would call it as lysin A, peptidase as does Supersulley mentioned in the first post above. Like Supersulley, it has conserved domain pfam 13529 and when blasted against Supersulley's lysin A, it has a score alignment of 129 (81% query coverage). Does this seem reasonable? Thanks Marie

Link to this post | posted 22 May, 2018 15:47
fogartym1	the second Octobien lysin A HHPRED result 114Kb

Link to this post | posted 22 May, 2018 15:46

fogartym1

I am also having problems deciding the best functional calls for Gordonia split lysin A genes. In the singleton phage Octobien14 the first lysin gene product shows evidence for being a peptidase domain - possibly C39-likeA - a subfamily of c39 peptidases. The functional call Lysin A, protease M15 domain just doesn't seem quite right. A more generic 'peptidase domain' might be a better fit? For the second lysin A gene, there is evidence for hydrolase: N-acetylmuramoyl-L-alanine amidase family. Would glycosyl hydrolase be the correct functional call here? Again, a less specific call like hydrolase domain feels safer! Thank you for any advice. HHPRED results are attached. Marie 91Kb

Link to this post | posted 20 Feb, 2018 16:10

fogartym1

This semester we are annotating Octobien14 - a Gordonia singleton. When using blastP to help inform our start sites many of the 1:1 alignments that we see are from proteins in bacterial hosts and not bacteriophage. In situations where there is a 1:1 alignment with a bacterial protein and all phage protein alignments are not 1:1, should we just document the bacterial protein alignment, the phage protein alignment, or both?

Link to this post | posted 26 Jan, 2018 20:57

fogartym1

A related question: For annotation of Gordiona phages in PECAAN, is there a preference to which GENEMARK file is uploaded to PECAAN and hence will ultimately be incorporated in the DNA MASTER file. We are using Gordonia bronchialis as our host for the GENEMARK input for PECAAN and I am now wondering if GENEMARK S is a better option. Which one does DNAM use as a default? I see some difference in gene mark calls between PECAAN and out auto annotated DNA master file

Link to this post | posted 26 Jan, 2018 20:57

fogartym1

A related question: For annotation of Gordiona phages in PECAAN, is there a preference to which GENEMARK file is uploaded to PECAAN and hence will ultimately be incorporated in the DNA MASTER file. We are using Gordonia bronchialis as our host for the GENEMARK input for PECAAN and I am now wondering if GENEMARK S is a better option. Which one does DNAM use as a default? I see some difference in gene mark calls between PECAAN and out auto annotated DNA master file

Link to this post | posted 26 Jan, 2018 20:57

fogartym1

A related question: For annotation of Gordiona phages in PECAAN, is there a preference to which GENEMARK file is uploaded to PECAAN and hence will ultimately be incorporated in the DNA MASTER file. We are using Gordonia bronchialis as our host for the GENEMARK input for PECAAN and I am now wondering if GENEMARK S is a better option. Which one does DNAM use as a default? I see some difference in gene mark calls between PECAAN and out auto annotated DNA master file

Link to this post | posted 25 Jan, 2018 15:57

fogartym1

We are seeing this too - which leads me to this question. For annotation of Gordiona phages in PECAAN, is there a preference to which GENEMARK file is uploaded to PECAAN and hence will ultimately be incorporated in the DNA MASTER file. We used Gordonia bronchialis as our host for the GENEMARK input for PECAAN and are now wondering if GENEMARK S is a better option. Which one does DNAM use as a default? Thanks Edited 25 Jan, 2018 15:58

Link to this post | posted 09 Jan, 2017 14:14
fogartym1	Where can we access the Web Phamerator from? I can't seem to find a link. Thanks