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by adding changes in color based on switches in subcluster the resulting tracks show a switch in color from the phage loaded as a profile and subsequent phages. This is because the profile phage does …
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- [x] curate depolymerase protein database (remove redundancies, construct tree,...)
- [ ] extend and curate depolymerase database by homology searches in IMG VR 3
- [ ] identify (blast) depolymeras…
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Hi,
I have been trying to use VIBRANT on linux. I installed it through Gitclone as I had trouble trying to install the usual way. I had the message saying vibrant was good to go but when I tried t…
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Thank you for the nice tool!
I would like use PHACTS to predict the life cycle of thousands of phages. Do you have any idea how could i do it?
Could I use it in our local cluter?
Thank you for y…
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- given a sequence, search (raw) datasets for instances of the virus (sort of the use case that C. Titus Brown describes in a couple of blog posts)
- from the zoo database, create an SBT, and go thro…
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From Jason:
Is the tool very specific for only the NCBI DB format?
Problem: is organism reliably identified in the headers of proteins?
Retool for Uniprot protein headers? These seem to always con…
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Hi!
I tried to run the mixed_examples data but the results is:
No phages found. There were either no scaffolds at least 1000bp or 4 ORFs (set minimum size), or the input file (-i) format (-f) was no…
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Hello,
Since your manuscript indicated the VIBRANT could recover both phages & archaeal viruses, I was wondering where I can find the information on if the identified viral scaffolds being bacterio…
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Hi, sean! Recently, I read your article 'Thousands of previously unknown phages discovered in whole-community human gut metagenomes'. And I am very curious about the phylogeny method in the article an…
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Hi all,
In my database some of the genomes use CTG as their start codon. This appears to not be a valid start codon in PhamDB. Is there any way I can edit the parameters of acceptable start codons …