TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions
...iptional regulations. To efficiently search for regulatory relationships from over 20 million pubmed articles, we used sentence-based text mining approach. TRRUST database also provid...2341 days ago
Rectangle Graph for Repeat Resolution in Genome Assembly
...Though the specific implementation of the idea of the rectangle graph approach is already included into the&...ugh RGM differs from the current implementation of the rectangle graph approach in SPAdes, in the future we p...2334 days ago
Alien_Hunter : prediction of putative Horizontal Gene Transfer (HGT) events
...the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). An IVOM approach exploits compositional biases...2324 days ago
Genome assembly stats plotting
...ct comparison of alternate assemblies. Tabular presentation allows direct comparison of exact values between assemblies, the limitations of this approach lie in the necessary omission...2272 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.2251 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
...genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original approach and its first implementation...2203 days ago
MIX: Combining multiple assemblies from NGS data
...sion. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length. The Mix algorithm, approach and results were published in...2203 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
SEX-DETector is a probabilistic method that relies on RNAseq data from a cross (parents and progeny of each sex) to infer autosomal and sex-linked genes (genes located o...2181 days ago
2175 days ago
HALC: High throughput algorithm for long read error correction
...at least one contig region, including its true genome region’s repeats in the contigs sufficiently similar to it (similar repeat based alignment approach) HALC was able to obtain 6...2172 days ago