Databases and Software
Databases and Softwaresparse-growth-curve: a Computational Pipeline for Parsing Cellular Growth Curves with Low Temporal ResolutionHere, we introduce a Python-based repository sparse-growth-curve, a software package designed for parsing cellular growth curves with low temporal resolution. The repository uses cell density and time data as the input, automatically separates different growth phases, calculates the exponential growth rates, and produces multiple graphs to aid in interpretation.
Databases and SoftwareDelila-PY, a Pipeline for Utilizing the Delila Suite of Software to Identify Potential DNA Binding MotifsPredicting potential DNA binding motifs is a critical part of understanding gene expression across all domains of life. Here, we report the development of Delila-PY, an easy-to-use pipeline to utilize the Delila suite to identify DNA binding motifs.
Databases and SoftwareThe Polyomavirus Episteme: A Database for ResearchersPolyomaviridae members are DNA viruses that infect a variety of species. Since the first polyomavirus was isolated in 1953, technological advancements have led to the discovery of many polyomaviruses in multiple species. The Polyomavirus Episteme curates data about each polyomavirus, drawing from public databases to present known taxonomic, genomic, and clinical information about polyomaviruses.
Databases and SoftwareViroMatch: A Computational Pipeline for the Detection of Viral Sequences from Complex Metagenomic DataViroMatch is an automated pipeline that takes metagenomic sequencing reads as input and performs iterative nucleotide and translated nucleotide mapping to identify viral sequences. We provide a Docker image for ViroMatch, so that users will not have to install dependencies.
Databases and SoftwareAn Improved Caulobacter crescentus Operon Annotation Based on Transcriptome DataCaulobacter crescentus is a model alphaproteobacterium with a well-studied genetic network controlling its cell cycle. Essential for such studies is an accurate map of the expressed features of its genome. Here, we provide an updated map of the expressed RNAs by integrative analysis of 5′ global rapid amplification of cDNA ends, transcriptome sequencing, rifampicin...
Databases and SoftwareCOnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus DatabaseWe introduce COnTORT (COmprehensive Transcriptomic ORganizational Tool), a publicly available program that retrieves all available gene expression data and associated metadata for an organism from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database. The data are compiled into text files that can be used for downstream...
Databases and SoftwareGenePiper, a Graphical User Interface Tool for Microbiome Sequence Data MiningAmplicon sequencing of the 16S rRNA gene is commonly performed for the assessment and comparison of microbiomes. Here, we introduce GenePiper, an open-source R Shiny application that provides an easy-to-use interface, a wide range of analytical methods, and optimized graphical outputs for offline microbiome data analyses.
Databases and SoftwareTwinBLAST: When Two Is Better than OneAnalysis of sequence read pairs can be essential for characterizing structural variation, including junction-spanning pairs of reads (JSPRs) suggesting recent lateral/horizontal gene transfer. TwinBLAST can be used to facilitate this analysis of JSPRs by enabling the visualization and curation of two BLAST reports side by side in a single interface.
Databases and SoftwaregndDb, a Database of Partial gnd Sequences To Assist with Analysis of Escherichia coli Communities Using High-Throughput SequencingThe use of culture methods to detect Escherichia coli diversity does not provide sufficient resolution to identify strains present at low levels. Here, we target the hypervariable gnd gene and describe a database containing 534 distinct partial gnd sequences and associated O groups for use with culture-independent...
Databases and SoftwareT-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom TreesThe Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.