User: Elendol

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Elendol0
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Posts by Elendol

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Comment: C: Ranking bacterial genomes using present and absent genes information
... Hi Joe, Yes that's what I do for a part on my project but working on a limited number of genomes. The downside of this method is it's a bit "too smart" I need to load all the genomes, perform the pangenome analysis and from there analysis the locus. I was doing something much simpler that would f ...
written 7 months ago by Elendol0
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Ranking bacterial genomes using present and absent genes information
... Hi, I started to work on this project a bit outside my usual area of expertise so I am not really aware of all the tools and algorithms (yet), so I thought I might find people with more experience here. How would you rank a list of genomes according to the presence or absence of certain genes of i ...
genome bacteria written 7 months ago by Elendol0
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Mash screen matching hashes interpretation
... Maybe a stupid question, but how do you interpret the hash count with mash screen? What threshold to use regarding the number of matching hashes? For example when using mash screen on PLSDB https://ccb-microbe.cs.uni-saarland.de/plsdb, if a contig gets only few matching hashes (~50) but a p-value ...
genome mash written 8 months ago by Elendol0
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Comment: C: A good enough up-to-date phosphorylation database?
... I did, but the data base didn't receive any update since 2010 apparently. ...
written 2.8 years ago by Elendol0
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A good enough up-to-date phosphorylation database?
... Hi, There are a lot of phosphorylation data bases out there, I would like to know which one is considered a gold standard, or at best good enough and up-to-date (as much as possible) data base of experimentally validated phosphoylation sites to use as reference against simple motif predictions. I'm ...
ptm database sequence protein written 2.8 years ago by Elendol0 • updated 2.8 years ago by Jean-Karim Heriche23k
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how to find lineage specific dissimilar regions in an alignment?
... Hello, I have protein alignments and a phylogenetic tree, we suspect that for some species in a (more or less) conserved region, the sequences vary whereas at the same positions for other species this region is well conserved. By looking at the alignment I found good candidates but I need a metho ...
phylogeny conservation alignment tree written 2.9 years ago by Elendol0 • updated 2.1 years ago by Biostar ♦♦ 20

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