GRASP-suite is a collection of tools and tutorials to perform and analyse ancestral sequence reconstruction.
Central to the GRASP-suite is Graphical Representation of Ancestral Sequence Predictions (GRASP), an ancestral sequence reconstruction tool capable of performing maximum likelihood analysis on very large data sets.
Jupyter notebook tutorials that give the user an environment to analyse and curate sequence data sets. Includes notebooks for automatic and iterative removal of sequences and notebooks to map and visualise exon structure on multiple sequence alignments.
We developed Graphical Representation of Ancestral Sequence Predictions (GRASP) to infer and explore ancestral variants of protein families with more than 10,000 members. GRASP uses partial order graphs to represent homology in very large datasets, which are intractable with current inference tools and may, for example, be used to engineer proteins by identifying ancient variants of enzymes.
Data consistency is necessary for effective bioinformatic analysis. SeqScrub is a web tool that parses and maintains consistent information about protein and DNA sequences in FASTA file format, checks if records are current, and adds taxonomic information by matching identifiers against entries in authoritative biological sequence databases.
Commercial biocatalysis requires robust enzymes that can withstand elevated temperatures and long incubations. Ancestral reconstruction has shown that pre-Cambrian enzymes were often much more thermostable than extant forms. Here, we resurrect ancestral enzymes that withstand ~30 °C higher temperatures and ≥100 times longer incubations than their extant forms.