GLANET: genomic loci annotation and enrichment tool

Otlu, Burcak
Firtina, Can
Keles, Sunduz
Tastan, Oznur
Motivation: Genomic studies identify genomic loci representing genetic variations, transcription factor (TF) occupancy, or histone modification through next generation sequencing (NGS) technologies. Interpreting these loci requires evaluating them with known genomic and epigenomic annotations.


LFM-Pro: a tool for detecting significant local structural sites in proteins
Sacan, Ahmet; Ozturk, Ozgur; Ferhatosmanoglu, Hakan; Wang, Yusu (Oxford University Press (OUP), 2007-03-15)
Motivation: The rapidly growing protein structure repositories have opened up new opportunities for discovery and analysis of functional and evolutionary relationships among proteins. Detecting conserved structural sites that are unique to a protein family is of great value in identification of functionally important atoms and residues. Currently available methods are computationally expensive and fail to detect biologically significant local features.
Finding differentially expressed genes for pattern generation
Abul, O; Alhajj, R; Polat, Faruk; Barker, K (Oxford University Press (OUP), 2005-02-15)
Motivation: It is important to consider finding differentially expressed genes in a dataset of microarray experiments for pattern generation.
iBioProVis: interactive visualization and analysis of compound bioactivity space
Dönmez, Ataberk; Rifaioğlu, Ahmet Süreyya; Atalay, Rengül; Atalay, Mehmet Volkan (Oxford University Press (OUP), 2020-08-15)
SUMMARY: iBioProVis is an interactive tool for visual analysis of the compound bioactivity space in the context of target proteins, drugs and drug candidate compounds. iBioProVis tool takes target protein identifiers and, optionally, compound SMILES as input, and uses the state-of-the-art non-linear dimensionality reduction method t-Distributed Stochastic Neighbor Embedding (t-SNE) to plot the distribution of compounds embedded in a 2D map, based on the similarity of structural properties of compounds and i...
RBPSponge: genome-wide identification of lncRNAs that sponge RBPs
HafezQorani, Saber; Houdjedj, Aissa; Arici, Mehmet; Said, Abdesselam; KAZAN, HİLAL (Oxford University Press (OUP), 2019-11-15)
The Summary: Long non-coding RNAs (lncRNAs) can act as molecular sponge or decoys for an RNA-binding protein (RBP) through their RBP-binding sites, thereby modulating the expression of all target genes of the corresponding RBP of interest. Here, we present a web tool named RBPSponge to explore lncRNAs based on their potential to act as a sponge for an RBP of interest. RBPSponge identifies the occurrences of RBP-binding sites and CLIP peaks on lncRNAs, and enables users to run statistical analyses to investi...
JOA: Joint Overlap Analysis of multiple genomic interval sets
Otlu, Burcak; Can, Tolga (Springer Science and Business Media LLC, 2019-03-08)
BackgroundNext-generation sequencing (NGS) technologies have produced large volumes of genomic data. One common operation on heterogeneous genomic data is genomic interval intersection. Most of the existing tools impose restrictions such as not allowing nested intervals or requiring intervals to be sorted when finding overlaps in two or more interval sets.ResultsWe proposed segment tree (ST) and indexed segment tree forest (ISTF) based solutions for intersection of multiple genomic interval sets in parallel...
Citation Formats
B. Otlu, C. Firtina, S. Keles, and O. Tastan, “GLANET: genomic loci annotation and enrichment tool,” BIOINFORMATICS, pp. 2818–2828, 2017, Accessed: 00, 2020. [Online]. Available: