BioStar
Bioinformatician
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Apollo: First instantaneous, collaborative genomic annotation editor available on the Web
By Jit 2471 days agogenomearchitect.github.io - Apollo is a plug-in for the JBrowse Genome Viewer. In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transposable elements; each annotation type has its own...MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic...
By Jit 1878 days agogithub.com - MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. Metaeuk combines the fast and sensitive homology search capabilities of MMseqs2 with a dynamic programming procedure to...Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)
By Abhimanyu Singh 3355 days agohttp://prodigal.ornl.gov/ - Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal...genoPlotR - plot gene and genome maps project!
By Abhimanyu Singh 2642 days agogenoplotr.r-forge.r-project.org - genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files. Features Linear...MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
By BioStar 1927 days agogithub.com - The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene lists without...FQC Dashboard: Integrates FastQC results into a web-based, interactive, and extensible FASTQ...
By Shruti Paniwala 1943 days agogithub.com - FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The...GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns
By Neel 2183 days agogdblab.com - GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction. GSP4PDB is part of the services provided by the Bioinformatic Group of the University of...RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes
By Abhi 3601 days agohttp://rast.nmpdr.org/ - The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes...PASA: Gene Structure Annotation and Analysis
By biogeek 2992 days agopasapipeline.github.io - PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation...HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes
By Jit 2971 days agowww.ncbi.nlm.nih.gov - HGT-Finder: (i) can be used for HGT detection in both prokaryotes and eukaryotes, (ii) can report a statistical P value for each gene to indicate how likely it is to be horizontally transferred, and (iii) is fully automated (requires...
