Python kmer-format

Open-source Python projects categorized as kmer-format
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Topics: Deep Learning Machine Learning Natural Language Processing NLP GPU
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Python kmer-format Projects

  • DNABERT

    DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

    • Project mention: [D] New to DNABERT | /r/MachineLearning | 2023-11-03

    If I want to get started, they said it's optional to pre-train (so you can skip to step 3). This is where I got tripped up: "Note that the sequences are in kmer format, so you will need to convert your sequences into that." From what I understand, you need to do this so that all of the sequences are the same length? So kmer=6 means all of the sequences are length 6? Someone suggested that I take the first nucleotide in the promoter and grab 3 nucleotides before and 3 nucleotides after (+/-3 bases). I don't think that's how the kmer thing works though? I tried replicating how I think it works down below (I got confused on the last row of the 'after' df). Please correct me if I'm wrong!

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NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).

Index

Project Stars
1 DNABERT 546

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