BioDB-Loader toolkit loads several bioinformatics databases into Lisp for facile processin. BioDB-Loader contains utilities for loading flatfiles from the Swiss-Prot, Prosite, Enzyme, EcoCyc, and MetaCyc databases.
ALSE (ALl SEquences) compares favorably against common motif-finding programs such as SeedSearch and MEME in all cases and performs very well, especially when each input sequence contains more than one binding site.
MAMOT (hidden MArkov MOdelling Tool) is a program that provides access to the classic algorithms used for HMM modelling and some useful non-standard options for applications such as modelling protein binding sites in DNA sequences and the recognition of protein domains.
::DEVELOPER
Frédéric Schütz (Mauro.Delorenzi@isb-sib.ch) and Mauro Delorenzi (Frederic.Schutz@isb-sib.ch)
OptiMage is a tool for producing 3D layouts of network data. It can work with simple interaction data (e.g. protein-protein interactions), but can also be used to visualize directed networks, phylogenetic trees or distance matrices (e.g. evolutionary distances between genes).
Twease is a web-based tool to search Medline. Twease indexes each word of Medline, supports relevance or chronological searches, helps you find articles related to a set of articles of interest and provides many more features that can transparently expand your search to help find you the information you are looking for.
Annotare is a tool for annotating biomedical investigations and resulting data. It is a stand-alone desktop application that features 1) a set of intuitive editor forms to create and modify annotations, 2) support for easy incorporation of terms from biomedical ontologies, 3) standard templates for common experiment types, 4) a design wizard to help create a new document, and 5) a validator that checks for syntactic and semantic violation
ExpressConverter is a file transformation tool that reads microarray data files in a variety of file formats and generates TIGR MultiExperiment Viewer file (.mev) as output so that the microarray data can be uploaded to the database with MADAM and analyzed with MIDAS and MEV.
MISA (MIcroSAtellite Identification Tool) allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases.
PRIME (PaRtition of Ion types of tandem Mass spectra)is a software for identification of b and y ions in tandem mass spectra, a key challenging problem in de novo sequencing. PRIME utilizes a feature that ions of the same and different types follow different mass-difference distributions to separate b from y ions correctly. We have formulated the problem as a graph partition problem.A linear integer-programming algorithm has been implemented to solve the graph partition problem rigorously and efficiently.