:: DESCRIPTION
pantherScore scores protein sequences against the entire PANTHER HMM library and analyze your sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
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.
::DEVELOPER
Bioinformatics Research Group of Hong Kong University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2006 Sep 15;22(18):2217-23. Epub 2006 Jul 26.
Finding motifs from all sequences with and without binding sites.
Leung HC, Chin FY.
:: DESCRIPTION
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)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MAMOT: hidden Markov modeling tool.
Schütz F, Delorenzi M.
Bioinformatics. 2008 Jun 1;24(11):1399-400. Epub 2008 Apr 25.
:: DESCRIPTION
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).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BJ Holden, JW Pinney, SC Lovell, GD Amoutzias and DL Robertson
An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network (2007)
BMC Bioinformatics 8:289
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
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
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Ravi Shankar et al.
Annotare – a tool for annotating high-throughput biomedical investigations and resulting data,
Bioinformatics (2010) doi: 10.1093/bioinformatics/btq462
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
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.
::DEVELOPER
Thomas Thiel @ the Plant Genome Resources Center (PGRC)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Theor Appl Genet. 2003 Feb;106(3):411-22. Epub 2002 Sep 14.
Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).
Thiel T, Michalek W, Varshney RK, Graner A.
:: DESCRIPTION
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.
::DEVELOPER
the Computational Systems Biology Laboratory at the University of Georgia
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
B. Yan, Y. Qu, F. Mao, V Olman, Ying Xu,
PRIME: A Mass Spectrum Data Mining Tool for De Novo Sequencing and PTMs Identification
Journal of Computer Science and Technology
