AIMC Topic: Sequence Analysis, DNA

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repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects.

Bioinformatics (Oxford, England) Dec 10, 2014
UNLABELLED: In order to develop powerful computational predictors for identifying the biological features or attributes of DNAs, one of the most challenging problems is to find a suitable approach to effectively represent the DNA sequences. To facili...
Oligonucleotides Support Vector Machine Sequence Analysis, DNA DNA Humans Software Computational Biology
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MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning.

DNA research : an international journal for rapid publication of reports on genes and genomes Nov 27, 2014
The assembly of multiple genomes from mixed sequence reads is a bottleneck in metagenomic analysis. A single-genome assembly program (assembler) is not capable of resolving metagenome sequences, so assemblers designed specifically for metagenomics ha...
Metagenome Humans Sequence Analysis, DNA Genome Software Support Vector Machine
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Novel natural vector with asymmetric covariance for classifying biological sequences.

Gene Aug 20, 2025
The genome sequences of organisms form a large and complex landscape, presenting a significant challenge in bioinformatics: how to utilize mathematical tools to describe and analyze this space effectively. The ability to compare relationships between...
Genomics Computational Biology Sequence Analysis, DNA Machine Learning Algorithms
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ReQuant: improved base modification calling by k-mer value imputation.

Nucleic acids research May 10, 2025
Nanopore sequencing allows identification of base modifications, such as methylation, directly from raw current data. Prevailing approaches, including deep learning (DL) methods, require training data covering all possible sequence contexts. These da...
Bacteriophage lambda Software Nanopore Sequencing Algorithms DNA CpG Islands Sequence Analysis, DNA Humans DNA Methylation Deep Learning
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PCVR: a pre-trained contextualized visual representation for DNA sequence classification.

BMC bioinformatics May 9, 2025
BACKGROUND: The classification of DNA sequences is pivotal in bioinformatics, essentially for genetic information analysis. Traditional alignment-based tools tend to have slow speed and low recall. Machine learning methods learn implicit patterns fro...
DNA Computational Biology Machine Learning Sequence Analysis, DNA Algorithms
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Precision DNA methylation typing via hierarchical clustering of Nanopore current signals and attention-based neural network.

Briefings in bioinformatics Sep 23, 2024
Decoding DNA methylation sites through nanopore sequencing has emerged as a cutting-edge technology in the field of DNA methylation research, as it enables direct sequencing of native DNA molecules without the need for prior enzymatic or chemical tre...
DNA Nanopores DNA Methylation Cluster Analysis Nanopore Sequencing Humans Neural Networks, Computer Sequence Analysis, DNA
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CSV-Filter: a deep learning-based comprehensive structural variant filtering method for both short and long reads.

Bioinformatics (Oxford, England) Sep 2, 2024
MOTIVATION: Structural variants (SVs) play an important role in genetic research and precision medicine. As existing SV detection methods usually contain a substantial number of false positive calls, approaches to filter the detection results are nee...
Software Algorithms Deep Learning Humans Genomic Structural Variation Sequence Analysis, DNA High-Throughput Nucleotide Sequencing
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BertSNR: an interpretable deep learning framework for single-nucleotide resolution identification of transcription factor binding sites based on DNA language model.

Bioinformatics (Oxford, England) Aug 2, 2024
MOTIVATION: Transcription factors are pivotal in the regulation of gene expression, and accurate identification of transcription factor binding sites (TFBSs) at high resolution is crucial for understanding the mechanisms underlying gene regulation. T...
Binding Sites Sequence Analysis, DNA DNA Computational Biology Transcription Factors Algorithms Software Deep Learning
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iM-Seeker: a webserver for DNA i-motifs prediction and scoring via automated machine learning.

Nucleic acids research Jul 5, 2024
DNA, beyond its canonical B-form double helix, adopts various alternative conformations, among which the i-motif, emerging in cytosine-rich sequences under acidic conditions, holds significant biological implications in transcription modulation and t...
Humans Machine Learning Internet Sequence Analysis, DNA Software DNA Nucleotide Motifs Algorithms
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PlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning.

Briefings in bioinformatics May 23, 2024
Plasmids are extrachromosomal DNA found in microorganisms. They often carry beneficial genes that help bacteria adapt to harsh conditions. Plasmids are also important tools in genetic engineering, gene therapy, and drug production. However, it can be...
Computational Biology Sequence Analysis, DNA Plasmids Software Algorithms Machine Learning
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