Home page for Miguel Andrade

I am the group leader of the Computational Biology and Data Mining group, member of the Faculty of Biology of the Johannes Gutenberg University in Mainz, and an affiliate investigator at the Ottawa Hospital Research Institute.



Development of Biocomputing resources

I collaborate in the development of Biocomputing algorithms and databases. Most of them are publicly available through web servers.


pSTR identify duplications of protein short tandem repeats (pSTRs) in protein families.
polyXY Search for regions of two amino acid types (polyXY) in datasets of protein sequences.
iOrME Sequence clusters of insect odorant receptors.
seqQscorer Automated quality control of NGS data using machine learning.
PolyX2 Search for homorepeats in datasets of protein sequences.


AnABlast Detect potential coding regions in DNA by sequence comparison.
ARD2 Identification of alpha-solenoid repeats (e.g. HEAT, armadillo) in protein sequences using a neural net. This is an update of ARD. [About]
BiasViz Visualization of amino acid biased regions in protein alignments. [Code]
Bluster Sequence similarity search against our collection of protein sequence clusters.
CABRA Clusters and annotates the results of a BLAST search. [About]
CAFE Detects chromosomal abnormalities from DNA microarray expression data. [About]
CellFinder Browse and compare images, gene and protein expression data from mammalian cells. [About]
DiseaseLinc Associate lincRNAs with diseases.
dAPE Annotates homorepeats (polyX) in protein sequence alignments.
FASTA Herder Clusters a set of protein sequences according to their similarity. [About]
FastaHerder2 Clustering for analysis of protein similarity. [About]
GAPI Explores a hyperbolic mapping of the human potein interaction network.
Génie Rank the genes of an organism according to a topic. [About]
GS2D Gene Set to Diseases identifies disease terms enriched in the bibliography of a set of genes.
HIPPIE Study and filter the network of human protein-protein interaction data. [About]
K2D2 See also K2D3. Predict protein secondary structure content from circular dichroism spectra. This is an update of k2d. [About]
K2D3 See also K2D2. Predict protein secondary structure content from circular dichroism spectra using theoretical spectra. [About]
LCT Represent the distribution of repeatability versus compositional bias in a protein sequence.
LipiDisease Associate lipids with diseases.
MAGA Analyse amino acid conservation in user defined groups of proteins from a multiple sequence alignment.
mBISON Finds enrichment of miRNA targets on lists of genes. [About]
Medline Ranker Score abstracts from Medline according to a training set of abstracts or a MeSH term. [About]
MGFR Detect markers segregating sample types in RNA-seq data.
MIPPIE Study and filter the network of mouse protein-protein interaction data.
NYCE Predict subcellular location of eukaryotic proteins based on their sequence. [About]
OrthoFind Obtains the orthologs and paralogs of a protein sequence. [About]
PESCADOR Extract and analyse a network of gene and protein interactions from a set of Medline abstracts. [About]
PlaToLoCo Analyse low complexity regions in protein sequences.
ProteinPathTracker Find selected orthologs to study the evolutionary path of a protein.
QiSampler QiSampler evaluates alternative scoring schemes of a list of items based on a very small set of positives.
REP2 Identification of protein repeats.
RES Scan a protein sequence for its repeatability.
sQanner Evaluate the distribution of polyQ stretches in a set of proteins.
Traitpedia A collaborative database of species traits.
uORFdb Query the literature on upstream open reading frame (uORF) biology. [About]


Some of these tools are dying (nothing is eternal!). If you are concerned about this please contact me. May be something can be done.

StemBase 2003-2008 A database of stem cell gene expression for data derived at the Ottawa Hospital Research Institute. Last active URL http://www.stembase.ca/
Alkemio 2014-2022 To rank chemical substances according to their relation to a biomedical topic. Last active URL http://cbdm-01.zdv.uni-mainz.de/~jfontain/cms/?page_id=319
PhyloView 2012-2014 Colour a phylogenetic tree according to taxonomy. Last active URL http://www.ogic.ca/projects/phyloview/
peer2ref 2012-2014 Find referees for a manuscript using some of its text (e.g. abstract). Last active URL http://peer2ref.ogic.ca/
Marker Server 2006-2014 Detection of stem cell markers using gene expression data analysis. Last active URL https://cbdm.mdc-berlin.de/~markerserver/
PDBpaint 2010-2014 Colour protein structures with sequence annotations. Last active URL http://cbdm.mdc-berlin.de/~pdbpaint
G2D 2002-2014 Candidate genes to inherited diseases derived by data mining. Last active URL http://www.ogic.ca/projects/g2d_2/
ARD 2008-2013 Updated as ARD2. Identification of alpha-rod repeats (e.g. HEAT, armadillo) in protein sequences using a neural net.
MLTrends 2009-2018 Graphs word and term usage trends in the Medline database of biomedical abstracts. Last active URL http://mltrends.ogic.ca/
Transcriptome Sailor 2006-2016 Examine a genomic region in mouse or human for 3' transcript ends according to EST evidence. Last active URL http://cbdm.mdc-berlin.de/tools/ts/
Probe2GO 2005-2016 Obtain extended GO annotations for Affymetrix probe sets. Last active URL http://cbdm.mdc-berlin.de/tools/p2g/
XplorMed 2001-2015 Analysis of queries in MEDLINE. Last active URL http://xplormed.ogic.ca/
Disease_KW 2000-2014 Get keywords associated to human disease from OMIM entries or from MEDLINE abstracts. Last active URL http://www.embl.de/%7Eandrade/papers/disease_kw
KAT 2003-2011 Keyword Annotation Tool: derive keywords from sets of references to the scientific literature. Last active URL http://www.bork.embl.de/kat/
AbXtract 1998-2004 Automatic Abstract eXtraction of keywords associated to protein function. Last active URL http://columba.ebi.ac.uk:8765/andrade/abx
GeneQuiz 1998-2007 Automatic large scale sequence analysis using a variety of DNA/protein databases and protein analysis methods. Analyses were performend during 1996-2003. Contact Christos Ouzounis for availability. The method was available at the EBI (1998-2004) and then at the Memorial Sloan-Kettering Cancer Center (2005-2007). Last active URL http://www.sander.ebi.ac.uk/genequiz/
k2d 2000-2014 Updated as K2D2. Prediction of protein secondary structure percentages from circular dichroism data. Last active URL http://www.bork.embl.de/%7Eandrade/k2d/
NAIL 2000-2014 Representation and linking of HMMer output. Last active URL http://www.bork.embl-heidelberg.de/NAIL/


Tel: +49-6131-39-21582
Fax: +49-6131-39-21589
email: Andrade@uni-mainz.de