Tools

HIPPIE: study and filter the network of human protein-protein interaction data. Alanis-Lobato et al., 2017

dAPE: annotates homorepeats (polyX) in protein sequence alignments. Mier and Andrade-Navarro, 2016

GeneSet2Diseases: calculates enrichment of associations to diseases on sets of human genes. Andrade-Navarro and Fontaine, 2016.

CABRA: Clusters and annotates the results of a BLAST search. Mier and Andrade-Navarro, 2016b.

FastaHerder2: uses clustering for analysis of protein similarity. Mier and Andrade-Navarro, 2016a.

OrthoFind: obtains the orthologs and paralogs of a protein sequence. Mier et al., 2015

mBISON: to find enrichment of miRNA targets on lists of genes. Gebhardt et al., 2015

Alkemio: ranking thousands of chemicals for any topics using document categorization. Gijón-Correas et al., 2014

CAFE: detects chromosomal abnormalities from DNA microarray expression data. Bollen et al. 2014

NYCE: predicts subcellular location of eukaryotic proteins based on their sequence. Mer and Andrade-Navarro, 2013

ARD2: identification of alpha-solenoid repeats (e.g. HEAT, armadillo) in protein sequences using a neural network. Fournier et al., 2013. ARD2 is an update of ARD: Palidwor et al., 2009

uORFdb: a literature database on upstream open reading frame (uORF) biology. Wethmar et al., 2013

CellFinder: study annotations, bibliography, gene and protein expression in stem cells and derivatives. Stachelscheid et al., 2013

PESCADOR: extract and analyse a network of gene and protein interactions from a set of Medline abstracts. Barbosa-Silva et al., 2011

PDBpaint: a visualization webservice to tag protein structures with sequence annotations. Fournier and Andrade-Navarro, 2011

QiSampler: evaluate alternative scoring schemes for list of items (e.g. genes) based on a very small set of positives. Fontaine et al., 2011

Génie: ranking all the genes of your favorite species for any topic in a few seconds using orthology information. Fontaine et al., 2011

MLTrends: graphs word and term usage trends in the Medline database of biomedical abstracts. Palidwor and Andrade-Navarro, 2010

MedlineRanker: flexible ranking of the biomedical literature in practical time. This tool allows searching the Medline database or filter a large set of abstracts for a given topic. Fontaine et al., 2009

Genes2Diseases: predict genes associated to inherited disease. Tremblay et al., 2008

pSILAC: database of proteomics measurements under the influence of various miRNAs. Selbach et al., 2008

K2D2: predict protein secondary structure content from circular dichroism spectra. Perez-Iratxeta and Andrade-Navarro, 2008

K2D3: Predict protein secondary structure content from circular dichroism spectra using theoretical spectra. Louis-Jeune et al., 2011

Marker Server: discover marker genes in sets of gene expression data. Currently you can examine a set of 80+ murine stem cell related samples. Krzyzanowski and Andrade-Navarro, 2007

BiasViz: represent amino acid bias in protein sequences from an alignment. Huska et al., 2007

StemBase: explore a database of gene expression data from stem cell samples. Porter et al., 2007

PhyloView: colour a phylogenetic tree according to taxonomy. Palidwor et al., 2006