User: nafizh

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nafizh0
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Posts by nafizh

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Comment: C: Proteins that cannot form biofilm?
... Essentially, yes, I am trying to detect proteins that are indispensable in forming biofilms. So, I need a negative set of protein sequences which definitely don't have that function. ...
written 15 months ago by nafizh0
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Proteins that cannot form biofilm?
... I am trying to build a machine learning training set for bacterial protein sequences that form biofilm, and that cannot. I collected the positive sequences from the GO ontology website but for negative sequences I am not sure which sequences to incorporate into my training set. Can anyone point me ...
gene bacteria protein microbiology written 15 months ago by nafizh0 • updated 15 months ago by Elisabeth Gasteiger1.6k
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What are some examples of non-homologous sequences having similar functions?
... I am trying to find some proteins that are non-homologous but functionally similar. But cannot seem to find concrete examples. Can someone please point out any resources or provide examples? ...
genome alignment sequence blast written 17 months ago by nafizh0 • updated 8 months ago by Biostar ♦♦ 20
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Comment: C: How to get negative training set if I don't know what constitutes negative?
... Yeah, I am only interested in finding out which ones belong to the positive set from new sequences. ...
written 2.5 years ago by nafizh0
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Comment: C: How to get negative training set if I don't know what constitutes negative?
... Sorry, maybe, I was not clear. My question was, during the testing, what if the test set has negative sequences from different areas than the negative sequences in the training set. Then can the classifier classify between the positive and the negative? Please, let me know, if you want me to clarify ...
written 2.5 years ago by nafizh0
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Comment: C: How to get negative training set if I don't know what constitutes negative?
... But then what happens, if my test set has sequences from different areas than what you mentioned? ...
written 2.5 years ago by nafizh0
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Comment: C: How to get negative training set if I don't know what constitutes negative?
... I have a set of experimentally verified sequences from bacteria that produce bacteriocins. That is my positive set. But I have no concrete evidence for what constitutes negative i.e. sequences that do not produce bacteriocins. ...
written 2.5 years ago by nafizh0
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How to get negative training set if I don't know what constitutes negative?
... I have some bacteria dna sequences as a positive training set by some specific function of theirs. My negative training set would be whatever that does not fall into this category of positive training set. But I do not know in a sure fire way if a sequence falls into this positive category or not. S ...
machine_learning sequence blast dna written 2.5 years ago by nafizh0
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How to interpret Glimmer scores?
... Hi, I am trying to find orfs with Glimmer. At the end it gives me a .predict file with the orfs and a corresponding raw score. When I look at the documentation, it says, "This is 100 times the per-base log-odds ratio of the in-frame coding ICM score to the independent (i.e., non-coding) model score. ...
glimmer gene-finding written 2.6 years ago by nafizh0

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