Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third generation sequencing platforms can lead to tra...ire long and accurate reads including de novo assembly, fusion and structural variation detection. In such cases rese...2085 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 Biosciences...nerated with a given GC content. It can consist of several chromosomes, whose structure...2084 days ago
2070 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 e...2065 days ago
STRUM: structure-based prediction of protein stability changes upon single-point mutation
STRUM is a method for predicting the fold stability change (ΔΔG) of protein m...y of features at different levels of sequence and structure properties. The unique charac...bination of sequence profiles with low-resolution structure...2064 days ago
GenomeThreader: Gene Prediction Software
GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach w...nal cDNA/EST and/or protein sequences are used to predict gene structure...2041 days ago
nQuire: a statistical framework for ploidy estimation using next generation sequencing
nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely t...2041 days ago
SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, b...f a network. A very efficient algorithm, based on the Disjoint Sets Data Structure...1972 days ago
Biotite: A general framework for computational biology
The package is open source and freely available at GitHub (https://github.c...sts of four sub packages: sequence, structure, databases, and application. The sequence and structure modules serve for the an...ocuses on working with sequence and structure...1966 days ago
GeneOverlap: An R package to test and visualize gene overlaps
Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modifica...llular mechanism that can pack and re-pack chromatin. By making the chromatin structure...1956 days ago