MULSEA – Mutual enrichment in aggregated ranked lists

MULSEA

:: DESCRIPTION

MULSEA (MUlti-list SElection algorithm) is a tool for identifying mutual enrichment in aggregated ranked lists with applications to gene expression regulation.

::DEVELOPER

Yakhini Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

MULSEA

:: MORE INFORMATION

Citation

Bioinformatics. 2016 Sep 1;32(17):i464-i472. doi: 10.1093/bioinformatics/btw435.
Mutual enrichment in aggregated ranked lists with applications to gene expression regulation.
Cohn-Alperovich D, Rabner A, Kifer I, Mandel-Gutfreund Y, Yakhini Z.

GOrilla – Gene Ontology enRIchment anaLysis and visuaLizAtion tool

GOrilla

:: DESCRIPTION

GOrilla is a web-based application that identifies enriched GO terms in ranked lists of genes, without requiring the user to provide explicit target and background sets. This is particularly useful in many typical cases where genomic data may be naturally represented as a ranked list of genes (e.g. by level of expression or of differential expression).

::DEVELOPER

Yakhini Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson and Zohar Yakhini.
GOrilla: A Tool For Discovery And Visualization of Enriched GO Terms in Ranked Gene Lists“,
BMC Bioinformatics 2009, 10:48.

ARTO – Analysis of Replication Timing and Organization

ARTO

:: DESCRIPTION

ARTO (Analysis of Replication Timing and Organization) uses signal processing methods to fit a constant piece-wise linear curve to the measured raw data. The software takes raw time of replication (ToR) measurement signals as input and outputs for each genomic location an estimate of its ToR and an association to CTR (constant ToR region) or TTR (Temporal Transition Region).

::DEVELOPER

Laboratory of Computational Biology at the Technion.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • MatLab

:: DOWNLOAD

  ARTO

:: MORE INFORMATION

Citation

Systematic determination of replication activity type highlights interconnections between replication, chromatin structure and nuclear localization.
Farkash-Amar S, David Y, Polten A, Hezroni H, Eldar YC, Meshorer E, Yakhini Z, Simon I.
PLoS One. 2012;7(11):e48986.

ATRHunter / ATRHunterPlus – Find Approximate Tandem Repeats in a Genomic Sequence

ATRHunter / ATRHunterPlus

:: DESCRIPTION

ATRHUNTER finds and displays approximate tandem repeats (ATR) in DNA sequences. An approximate tandem repeat (ATR) in a genomic sequence is a string of nucleotides repeated consecutively at least twice with some small differences between the repeated copies

ATRHunter Online Version

::DEVELOPER

Laboratory of Computational Biology , Technion

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 ATRHUNTER

:: MORE INFORMATION

Citation

Wexler Y, Yakhini Z, Kashi Y, Geiger D.
Finding Approximate Tandem Repeats in Genomic Sequences
J Comput Biol. 2005 Sep;12(7):928-42

ENViz 3.1.5 – Integrated Statistical Analysis and Visualization of Sample-Matched Data with Multiple Data Types

ENViz 3.1.5

:: DESCRIPTION

ENViz (Enrichment Analysis and Visualization) is a Cytoscape app that performs joint enrichment analysis of two types of sample matched datasets in the context of systematic annotations.

::DEVELOPER

Agilent Laboratories

:: SCREENSHOTS

ENViz

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 ENViz

:: MORE INFORMATION

Citation

ENViz: a Cytoscape App for integrated statistical analysis and visualization of sample-matched data with multiple data types.
Steinfeld I, Navon R, Creech ML, Yakhini Z, Tsalenko A.
Bioinformatics. 2015 Jan 9. pii: btu853

DRIMust 1.0 – Discovering Ranked Imbalanced Motifs using suffix trees

DRIMust 1.0

:: DESCRIPTION

DRIMUST is a software implementation of a new statistical and algorithmic approach that we developed to enable efficient motif searches, covering a broader range of motif spaces comparing with state of the art motif searching tools. In particular, DRIMUST can efficiently search for variable gapped motifs, long motifs and motifs over large alphabets. The motif structure that DRIMUST searches comprises two half sites separated by a gap, that can be of a variable length.

::DEVELOPER

Yakhini Lab and the Mandel-Gutfreund Lab, at the Technion.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

DRIMust

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W174-9. doi: 10.1093/nar/gkt407. Epub 2013 May 17.
DRIMust: a web server for discovering rank imbalanced motifs using suffix trees.
Leibovich L1, Paz I, Yakhini Z, Mandel-Gutfreund Y.

Limor Leibovich, Zohar Yakhini:
Efficient motif search in ranked lists and applications to variable gap motifs.
Nucl. Acids Res. (2012) 40 (13): 5832-5847.

UnMeRFi – Under-Methylated Region Finder

UnMeRFi

:: DESCRIPTION

UnMeRFi (Under-Methylated Region Finder) estimates under-methylated regions in an unspecified DNA sequence. The program works by using a moving window (the size of which can be specified by the user) and by assessing the likelihood of that window to be under-methylated. As a final step windows passing the threshold  are joined to form contiguous under-methylated regions.

::DEVELOPER

Yakhini Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java

:: DOWNLOAD

 UnMeRFi

:: MORE INFORMATION

Citation

Straussman et al
Developmental programming of CpG island methylation profiles in the human genome
Nature Structural & Molecular Biology 16, 564 – 571 (2009)

ProbeSpec – Map Specificity of all Candidate Probes for a Given Sequence

ProbeSpec

:: DESCRIPTION

ProbeSpec is a utility for mapping the specificity of all candidate probes for a given sequence (e.g. transcript) against a background containing a large set of sequences (e.g. a transcriptome). Probe specificity is determined by the subsequence in the background that is most similar to its target, the specificity being set as the number of mismatches between the probe and the closest non-specific background sequence.

::DEVELOPER

Laboratory of Computational Biology , Technion

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ProbeSpec

:: MORE INFORMATION

Citation

Doron Lipson, Peter Web, Zohar Yakhini (2002)
Designing Specific Oligonucleotide Probes for the Entire S. cerevisiae Transcriptome
WABI ’02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics

DRIM – Discover Motifs in a list of ranked DNA sequences

DRIM

:: DESCRIPTION

DRIM (Discovery of Rank Imbalanced Motifs) is a tool for discovering short motifs in a list of nucleic acid sequences. DRIM was originally developed for DNA sequences and successfully applied on ChIP-chip and CpG methylation data. The current version has enhanced functionality and can be applied for both DNA and RNA. This new version was used to predict UTR motifs and Splicing Factor binding motifs based on RIP-Chip or CLIP data.
From a mathematical point of view, DRIM identifies subsequences that tend to appear at the top of the list more often than in the rest of the list. The definition of TOP in this context is flexible and driven by the data. Explicitly – DRIM identifies a threshold at which the statistical difference between top and rest is maximized. An exact p-value for the optimized event is also provided.

::DEVELOPER

Yakhini Lab and the Mandel-Gutfreund Lab, at the Technion.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DRIM

:: MORE INFORMATION

Citation

E. Eden, D. Lipson, S. Yogev & Z. Yakhini.
Discovering Motifs in Ranked Lists of DNA Sequences,
PLoS Computational Biology, 2007.

homoTarget – Prediction of microRNA targets in Homo Sapiens

homoTarget

:: DESCRIPTION

HomoTarget is a new algorithm for prediction of microRNA targets in Homo sapiens.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

HomoTarget

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 HomoTarget

:: MORE INFORMATION

Citation:

Genomics. 2012 Nov 19. pii: S0888-7543(12)00213-3. doi: 10.1016/j.ygeno.2012.11.005. [Epub ahead of print]
HomoTarget: A new algorithm for prediction of microRNA targets in Homo sapiens.
Ahmadi H1, Ahmadi A, Azimzadeh-Jamalkandi S, Shoorehdeli MA, Salehzadeh-Yazdi A, Bidkhori G, Masoudi-Nejad A