Reference-free prediction of rearrangement breakpoint reads
lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of...2263 days ago
GMOL: An Interactive Tool for 3D Genome Structure Visualization
GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.2250 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
EvidentialGene is a genome informatics project, "Evidence D...ction refers to the combination of classical gene prediction, and more recent gene assembl...ethods involve using available best-of-breed gene prediction and assembly software, combin...2202 days ago
GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.2177 days ago
2174 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpret...2187 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads....s to both the contigs and reference genome, and then constructs a novel data structure...2143 days ago
SimLoRD: A read simulator for third generation sequencing reads
SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Bioscience...erated with a given GC content. It can consist of several chromosomes, whose structure...2096 days ago
Ensembl Variation - Calculated variant consequences
For each variant that is mapped to the reference genome, we identify all overlapping Ensembl transcripts. We then use a rule-based approach to predict the effects that ea...2077 days ago
STRUM: structure-based prediction of protein stability changes upon single-point mutation
...n a variety of features at different levels of sequence and structure properties. The unique charac...is the combination of sequence profiles with low-resolution structure models from protein structure prediction, which helps enhance the robu...2077 days ago