ACRE is a JAVA-based tool that enumerates all the biochemical reaction
networks that consist of user-created nodes from user-selected modules under
Dragon DT Optimizer (DDTO)
GA based optimizer of decision tree parameters and structure
Dragon Extractor of Methylated Genes in Diseases (DEMGD) was developed for
mining of associations between methylated genes and diseases from free text
abstracts submitted by users. DEMGD presents the extracted associations in
summary tables and full reports in addition to evidence tagging of text with
respect to genes, diseases and methylation words. DEMGD allows research
scientists to extract methylated genes and diseases associations efficiently and
from the most recent literature.
Combining position weight
matrices and document-term matrix for efficient extraction of associations of
methylated genes and diseases from free text. Bin Raies A, Mansour H,
Incitti R, Bajic VB. PLoS One. 2013 Oct 16;8(10):e77848. doi:
Dragon Feature Selector Based on Biclustering (DFSBBC)
Dragon Text Mining PWMs Generator (DTMPG) was developed for generating
Position Weight Matrices (PWMs) from free text sentences. Also, DTMPG provides
functionalities to normalize the generated PWMs from text and use these matrices
to compute matching scores for sentences. Using DTMPG, you can view your input
data, the generated PWMs and the computed matching scores.
Using a novel methodology, this tool predicts the functional class of a
binding partner of transcription factor (TF) or transcription co-factor (TcoF).
It consists of two models. Model 1 predicts if the interacting partner of a TF
is TcoF or not. Model 2 predicts if the interacting partner of a TcoF is TF or
for predicting a functional class of proteins in transcription factor
complexes. Piatek MJ, Schramm MC, Burra DD, Binshbreen A, Jankovic BR,
Chowdhary R, Archer JA, Bajic VB. PLoS One. 2013 Jul 12;8(7):e68857. doi:
The DragonWFS is a feature selection (FS) web-tool based on the randomized
wrapper models. It is designed for researchers who deal with high dimensional
data and it is applicable to a variety of applications coming from the broad
biological and biomedical research fields.
DWFS: a wrapper feature
selection tool based on a parallel genetic algorithm. Soufan O,
Kleftogiannis D, Kalnis P, Bajic VB. PLoS One. 2015 Feb 26;10(2):e0117988. doi:
This tools has two components, one for NMR slice picking and the other one
for resonance assignment based on picked sliced. The required inputs are
CBCACONH.ucsf and HNCACB.ucsf.