Questions tagged [features]
The features tag has no usage guidance.
13
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Are there computational tools to extract features of DNA sequences?
I am looking for tools to extract features from short DNA sequences. For example, entropy, complexity, GC-content, etc.
I have found the generateFeatures.py script from the PyFeat repo, but is there ...
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3
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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 ...
- 910
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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 ...
- 527
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43
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Reduce Overfit by removing insignificant proteins through PSEA analysis
I'm training a ML model for disease prediction using protein composition as input, but overfit is present. While looking to remove proteins and reduce multi-correlation, as remove composition ...
2
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1
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Differentiating molecules based on peptide sequence? How to annotate?
I want to differentiate between classical class I and non classical class I MHC molecules in a model organism using well conserved structural features within classical MHC I molecules (eg intradomain ...
- 105
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1
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40
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Help with finding an unsupervised learning algorithm for RNA sequence/structure pattern identification
I have a bunch of RNA sequences (and their optimal secondary structures) and their corresponding energy values (measured by mean free energy) and I'm trying to find a way to identify features (...
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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 ...
0
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1
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multiplatt from indicspecies package not producing results for all groups
Based on presence absence data, I'm attempting to find indicator species for different sample sites. I have 25 different groups or "clusters" as I've labelled them. Running the R code below, ...
- 171
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93
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Extract features from fasta sequences and train the classifier
I am new to the bioinformatics field. I have positive and negative protein sequences for acetylation PTM. Now, I want to train a classifier, say SVM. What will be the next step? How can I convert ...
- 101
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37
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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, ...
- 179
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81
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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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248
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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 ...
- 2,232
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What are the fastest way of feature selection in R for large dataset in Machine Learning?
I have about 100 data sets with over 100,000 rows and 27 predictor variables and multiple response variable on each dataset. I want to select the most essential Features for these datasets. I used ...
- 319