Questions tagged [features]

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Feature extraction methods that can handle inconsistent numbers of atoms for molecular dynamics

I want to compare the protein dynamics ) pH 7 versus pH 3, or ) wild type versus mutant The protein will have slightly different number of atoms at each condition, due to protonation or mutation, ...
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Selecting genes with more contribution from PCA

I have RNA-seq data in response to treatment vs non response; By machine learning I selected three principle components likely can predict the response based on the gene expression. Now I have ...
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2answers
147 views

Is there a JSON-based genomic feature format?

There's a variety of formats for storing genomic features (e.g. Genbank, GFF, GTF, Bedfile) but all of the ones that I'm familiar with use either a custom format (Genbank) or a CSV with defined column ...
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How to predict protein binding to ligands?

I want to predict from protein sequence if the protein binds to metal, nuclear or small ligand. How can I do this ? Which features are relevant if I want to use them in a machine learning algorithm ?
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1answer
206 views

What is Feature Barcoding technology?

I heard the term Feature Barcoding a lot so I find resources to understand it. I have read docs of 10xgenomics and I see that ...
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1answer
84 views

How can the Autocovariances, autocorrelations, and autocorrelation coefficients be calculated from a Protein Amino Acid Sequence?

Given a normal protein sequence with the 20 standard amino acids, how can the 'Autocovariances', 'autocorrelations', and 'autocorrelation coefficients' of the sequence be calculated? What is meant by ...