Mercator: Multiple Whole-Genome Orthology Map Construction
...within multiple genomes. The term "syntenic" is often used to describe regions of multiple genomes that are...ly, given K genomes, we would like to identify all orthologous genomic regions as well as paralogous regions...1459 days ago
1450 days ago
The wavefront alignment (WFA) algorithm
The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage ofhomologous regions between the sequences to accelerate the alignment process. As oppose...1420 days ago
PhiSpy: PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes
...hages in Bacterial (and probably Archaeal) genomes. Given an annotated genome it will use several approaches to identify the most likely prophage regions. Initial versions of PhiSpy...1417 days ago
Sibelia: A comparative genomics tool
...evolutionary and genome rearrangement studies for multiple strains of microorganisms. Sibelia is useful in finding: (1) shared regions, (2) regions that present in one group of...1365 days ago
RosettaAntibodyDesign (RAbD): A general framework for computational antibody design
...late function. The framework is based on rigorous bioinformatic analysis and rooted very much on our recent clustering of antibody CDR regions. It uses the North/Dunbr...1336 days ago
1299 days ago
URMAP, an ultra-fast read mapper
....998, sensitivity 0.982 and F-measure 0.990) with the strelka2 caller. However, GIAB reference variants are shown to be biased against repetitive regions which are difficult to map an...1296 days ago
MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
...p;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 an ...1269 days ago
gggenomes: A grammar of graphics for comparative genomics
gggenomes is a versatile graphics package for comparative genomics. It extends the popular R visualization packageggplot2 by adding dedicated plot functions for genes, syntenic regions, etc. and verbs to manipulate the plot to, for example, quickly zoom in into gene neighborhoods.1201 days ago