Tag: K-mer

A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches

BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Finding fuzzy seed matches enable BLEND to find both 1) exact-matching seeds…

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ncRNA | Free Full-Text | Common Features in lncRNA Annotation and Classification: A Survey

CONC 2006 SVM Eukaryotes (both protein-coding and non-coding genes) peptide length, amino acid composition, predicted secondary structure content, mean hydrophobicity, percentage of residues exposed to solvent, sequence compositional entropy, number of homologues, alignment entropy 10-fold CV on protein-coding: F1-score: 97.4% ☼ Precision: 97.1% ☼ Recall: 97.8% ◙ On non-coding: F1-score:…

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Intepreting kmer spectrum

Intepreting kmer spectrum 0 Could someone provide an intuitive description of how to inerpret a k-mer spectrum? I understand that the plot shows how many kmers appear a certain number of times, but could someone describe to me what valuable information we can gain from visualizing kmer counts this way?…

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Assembling all transcripts for an individual gene? (using single sequence to seed the assembly)

Assembling all transcripts for an individual gene? (using single sequence to seed the assembly) 0 Let’s say I have a candidate gene and I believe that in an individual sample, the genome sequence differs from the reference which then interferes with alignment. Is there a way for me to do…

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DNA Sequence Classification Based on Milvus

Introduction DNA sequencing is a popular concept in both academic research and practical applications, such as gene traceability, species identification, and disease diagnosis. Whereas all industries starve for a more intelligent and efficient research method, artificial intelligence has attracted much attention, especially from the biological and medical domains. More and…

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Where can I get ?or how can I make a mappability track for hg38 assembly

Where can I get ?or how can I make a mappability track for hg38 assembly 2 Lucky you @manojmumar_bhosale I worked on similar problem recently and therefore have the bash script you can use. Required tools: GEM libary from here UCSC’s wigToBigWig from here (I chose binary for Linux 64…

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a k-mer counter in Rust using the rust-bio and rayon crates

Tool:krust: a k-mer counter in Rust using the rust-bio and rayon crates 0 I hope this isn’t inappropriate as a Share a Tool post, it’s more about getting feedback on and seeing if anybody here is interested in this project: github.com/suchapalaver/krust It’s a k-mer counter in written in Rust. I’ve…

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Prevalence and Molecular Characteristics Based on Whole Genome Sequenc

Introduction Tuberculosis, caused by Mycobacterium tuberculosis, remains one of the top 10 causes of death worldwide and the leading cause of death from a single infectious agent (ranking above HIV/AIDS).1 In 2020, World Health Organization (WHO) reported that 7.1 million people with tuberculosis were newly diagnosed and notified in 2019,…

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The Biostar Herald for Tuesday, August 17, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by lakhujanivijay,…

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k-mer counters – presence/absence matrix

k-mer counters – presence/absence matrix 2 Hi lizabe, You’re right that this tutorial is out of date. The –matrix option is no longer valid as an option to jellyfish count. However, I don’t think it’s original intent was to do what you wanted anyway. It doesn’t write out a binary…

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