The ecocyc database
EcoCyc is a bioinformatics database available at EcoCyc. org that describes the genome
and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the …
and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the …
BERT-Promoter: An improved sequence-based predictor of DNA promoter using BERT pre-trained model and SHAP feature selection
A promoter is a sequence of DNA that initializes the process of transcription and regulates
whenever and wherever genes are expressed in the organism. Because of its importance in …
whenever and wherever genes are expressed in the organism. Because of its importance in …
[PDF][PDF] Automatic annotation of microbial genomes and metagenomic sequences
VSA Salamov, A Solovyevand - Metagenomics and its …, 2011 - researchgate.net
We have developed Fgenesb_annotator pipeline that provides completely automatic and
comprehensive annotation of microbial genomic sequence. The pipeline identifies protein …
comprehensive annotation of microbial genomic sequence. The pipeline identifies protein …
Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks
RK Umarov, VV Solovyev - PloS one, 2017 - journals.plos.org
Accurate computational identification of promoters remains a challenge as these key DNA
regulatory regions have variable structures composed of functional motifs that provide gene …
regulatory regions have variable structures composed of functional motifs that provide gene …
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine
Background MicroRNAs (miRNAs) are a group of short (~ 22 nt) non-coding RNAs that play
important regulatory roles. MiRNA precursors (pre-miRNAs) are characterized by their …
important regulatory roles. MiRNA precursors (pre-miRNAs) are characterized by their …
Predicting human microRNA-disease associations based on support vector machine
The identification of disease-related microRNAs is vital for understanding the pathogenesis
of disease at the molecular level and may lead to the design of specific molecular tools for …
of disease at the molecular level and may lead to the design of specific molecular tools for …
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions
RegulonDB is the internationally recognized reference database of Escherichia coli K-12
offering curated knowledge of the regulatory network and operon organization. It is currently …
offering curated knowledge of the regulatory network and operon organization. It is currently …
T4-related bacteriophage LIMEstone isolates for the control of soft rot on potato caused by 'Dickeya solani'
EM Adriaenssens, J Van Vaerenbergh… - PloS one, 2012 - journals.plos.org
The bacterium 'Dickeya solani', an aggressive biovar 3 variant of Dickeya dianthicola,
causes rotting and blackleg in potato. To control this pathogen using bacteriophage therapy …
causes rotting and blackleg in potato. To control this pathogen using bacteriophage therapy …
Genomic benchmarks: a collection of datasets for genomic sequence classification
Background Recently, deep neural networks have been successfully applied in many
biological fields. In 2020, a deep learning model AlphaFold won the protein folding …
biological fields. In 2020, a deep learning model AlphaFold won the protein folding …