SpeedSeq is an open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement.
Knime4Bio is a set of custom nodes for the KNIME (The Konstanz Information Miner) graphical workbench, for analysing NGS data without the requirement of programming skills.
HTSmix represents the structure of signals in the screen using linear mixed models, normalizes and summarizes the phenotypes to make them comparable across samples, and outputs a list of hits while controlling the False Discovery Rate. The methodology is appropriate for experimental designs with at least two control samples profiled throughout the screen.
‘buccaneer‘ (BUild Connected C-Alphas, Nautical Excuse for Eponym Required) performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target.
‘Nautilus‘ (from Greek ναυτίλος, ‘sailor’) is a program for automatic model building of nucleotide structures in electron density maps. It will trace a map with no model, extend an existing model, or add nucleotide chains to an existing non-nucleotide model.
Lutefisk is software for the de novo interpretation of peptide CID spectra.High quality tandem mass spectra of peptides are often obtained for which no exact database match can be made. Consequently, we are faced with the question of whether the protein under investigation is novel, or if the non-matching spectra are due to less exciting prospects such as inter-species variation, database sequence errors, or unexpected proteolytic cleavages. To begin addressing this problem we perform a de novointerpretation of the CID spectra using the computer program Lutefisk; however, any such interpretations nearly always yield multiple sequence candidates, where it is often difficult or impossible to distinguish the correct sequence from the incorrect ones. The variations between candidate sequences are often minor and typically involve dipeptide inversions, swapping of dipeptides of the same mass, replacements of dipeptides with single amino acids of the same mass, and replacements of amino acids by dipeptides of the same mass. We use the multiple sequence candidates produced by Lutefisk as query sequences in a second program, CIDentify. CIDentify is a version of Bill Pearson’s FASTA algorithm modified by Alex Taylor to accommodate MS nuances such as multiple query sequences, ambiguous dipeptides and isobaric mass equivalencies.