Alien_Hunter : prediction of putative Horizontal Gene Transfer (HGT) events
Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local ...Tags: prediction, putative, Horizontal, Gene, Transfer, HGT, events, Alien, Hunter, Alien_hunter
2324 days ago
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 the number of neighboring reads. When applied to a dataset with a sequencing depth of 100×, it finds ∼88% of the bre...Tags: Reference-free, prediction, rearrangement, breakpoint, reads
2264 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.Tags: GLEAN, unsupervised, learning, integrate, gene, structure, evidence, prediction
2178 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 molecules upon single-point nsSNP mutations. STRUM adopts a gradient boosting regression approch to train the Gibbs free-energy changes on a variety of features at different levels of sequence and structure pr...Tags: STRUM, structure-based, prediction, protein, stability, changes, single-point, mutation
2078 days ago