Link to this post | posted 12 Jun, 2018 18:52
kklyczek	Tammy, Thanks for sharing these! Karen Edited 12 Jun, 2018 18:54

Link to this post | posted 07 Mar, 2018 04:17

kklyczek

The tape measure protein (Fork_Draft_54) and the tail assembly chaperone proteins (Fork_Draft_52 and 53) were identified based on blastp homology with AQ phages (Molivia_38-40). There is a slippery sequence near the end of Fork_Draft_52, TTTTTTC (as described for phage SPP1 in the Wu 2014 paper, https://www.ncbi.nlm.nih.gov/pubmed/15469818). The attached screen shot of the 6-frame translation shows this sequence; a -1 shift at 25657 would shift to the reading frame of Fork_Draft_53. This sequence is conserved in all of the cluster ED genomes. The AQ phage genomes have a similar overall architecture to the ED phage genomes, with long direct repeats and a similar organization of structural genes. They may be helpful in identifying other ED gene functions via synteny. 231Kb

Link to this post | posted 06 Mar, 2018 23:39

kklyczek

These genomes have one reverse gene, located near the right end - see Maggie_21. Autoannotation usually misses these and instead calls a small forward gene in that location. The forward gene should be deleted, and instead insert the reverse gene, which will have blast hits to HTH DNA binding domain proteins. Autoannotation sometimes calls a different reverse gene, entirely overlapping a forward gene, near the right end. That reverse gene (seen in some current drafts, e.g. Copper_Draft_24) should be deleted. Edited 08 Mar, 2018 14:15

Link to this post | posted 13 Jan, 2018 16:23

kklyczek

Hi Steve, The new annotation guide has a section on genome comparisons. The direct link is https://seaphagesbioinformatics.helpdocsonline.com/article-89 (may require login in), or go to Mechanics > DNA Master > DNA Master Genome Comparison Tool in the left panel. The guide suggests searching by accession number. But if the NCBI search is not working for some reason, you can also add genomes to the database by opening a .dnam file (or opening a fasta file and auto annotating) and using the Genome menu > Add to database. Then use Tools > Genome comparison > Manual to select genomes to analyze. Click on each genome and click the Add button, then click Analyze. ANIs are found in the Pairwise summaries tab. Note that the default is to show 16S identity, which will be zero for phage genomes. Select Average Nucleotide Identity from the pull-down menu. (The map comparison tab is also super useful - you can create a map from a modified .dnam file and compare it to other phages.) Karen

Link to this post | posted 22 Dec, 2017 03:46

kklyczek

Evan Merkhofer I have a non-installation question about DNA Master WINE. We're going to try to use the WINE version this year; last year my IT department tried to use a network-based virtual interface so students didn't have to install a virtual machine and windows, and it was not very successful. I can run WINE on my Mac (Yosemite), but how do people resize the gene list in the features window? I cannot seem to right-click using my MacBook Air trackpad, has anyone found a workaround? Hi Evan, This issue came up for a few folks at the bioinformatics workshop. What seemed to work is to change the settings in System Preferences > Trackpad to turn on the two-finger "secondary" click (see screen shot attached) - that appears to be the equivalent of a right click. Karen

Link to this post | posted 12 Dec, 2017 14:03
kklyczek	Debbie shared this paper at the bioinformatics workshop. It provides very useful background on programmed frame shifts and other recoding in phages: http://www.cell.com/trends/genetics/fulltext/S0168-9525(06)00024-2 Enjoy! Karen Edited 12 Dec, 2017 14:04

Link to this post | posted 27 Aug, 2017 15:25

kklyczek

Hi Jordan, I am also reviewing C1 phages and was wondering about this. In GenBank the wraparound genes are labeled as "misc_feature" but that is not a menu option in DNA Master. I think "misc_signal" is something different? I checked a few C1 phages submitted recently and the DNAM files label the wraparound genes as "cds" with 2 regions, sometimes with an explanation in the Notes window. GenBank must add the "misc_features" tag? This is what is looks like in the final documentation: CDS join(154634. .155205;1. .4) /gene="271" /product="Hypothetical Protein" /locus tag="SEA_AUDRICK_271" /note=circularly permuted genome; selection of sequence origin for linear molecule results in coding region disruption Karen

Link to this post | posted 22 Aug, 2017 20:06
kklyczek	I am reviewing the A2 phage Anselm, and the annotators asked about a gene at 49017-49085 (rev) that matches RedRock_87. It is only 69 bp long and there is no smeg coding potential. I would be inclined to delete it, but RedRock is a well-studied phage. It looks like many other A2 phages have a gap at this location.

Link to this post | posted 16 Aug, 2017 17:30
kklyczek	It has strong homology to the N-terminal half of the large terminase subunit, including the ATPase domain. It was identified as a terminase in the cluster J paper, though it may play some other role in phage assembly.

Link to this post | posted 16 Aug, 2017 13:50
kklyczek	So for the cluster J phages that have the the Baka_2 homologue, are we calling that terminase (not small or large subunit, just terminase)? Karen