ACEScan 1.0 – Prediction of Conserved Alternatively Spliced Exons from pairs of Conserved Mouse/Human Exons

ACEScan 1.0

:: DESCRIPTION

ACEScan is a webtool of identification and analysis of alternative splicing events conserved in human and mouse.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Yeo, G., Van Nostrand, E., Holste, D., Poggio, T. and Burge, C. B. (2005).
Identification and analysis of alternative splicing events conserved in human and mouse.
Proc. Natl. Acad. Sci. USA 102, 2850-2855

ApoCanD – Database of Human Apoptotic Proteins in the Context of Cancer

ApoCanD

:: DESCRIPTION

ApoCanD is a database comprises of crucial information of apoptosis proteins in the context of cancer.This database will facilitate the research community working in the field of apoptosis and cancer.

::DEVELOPER

ApoCanD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ApoCanD: Database of human apoptotic proteins in the context of cancer.
Kumar R, Raghava GP.
Sci Rep. 2016 Feb 10;6:20797. doi: 10.1038/srep20797.

HumCFS – A Database Of Human Chromosomal Fragile Sites

HumCFS

:: DESCRIPTION

HumCFS is a manually curated database of human chromosomal fragile sites. HumCFS provides useful information about 125 human chromosomal fragile sites and their association with 4921 human protein-coding genes and 917 human miRNA’s.

::DEVELOPER

HumCFS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

HumCFS: a database of fragile sites in human chromosomes.
Kumar R, Nagpal G, Kumar V, Usmani SS, Agrawal P, Raghava GPS.
BMC Genomics. 2019 Apr 18;19(Suppl 9):985. doi: 10.1186/s12864-018-5330-5.

PHDcleav – Prediction of Human Dicer Cleavage

PHDcleav

:: DESCRIPTION

PHDcleav is a webserver to predict Dicer cleavage sites in pre-miRNA. Dicer, an RNase III enzyme, plays vital role in RNA interference pathway, processes both pre-miRNAs (precursor microRNAs) and double-stranded (ds) RNAs to generate effector molecules. Thus it is very important to know true Dicer processing sites in the pre-miRNA molecules to understand the RNA interference pathway.

::DEVELOPER

PHDcleav team 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 14:S9. doi: 10.1186/1471-2105-14-S14-S9. Epub 2013 Oct 9.
PHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors.
Ahmed F, Kaundal R, Raghava GP.

LocFuse – Human protein-protein Interaction Prediction

LocFuse

:: DESCRIPTION

LocFuse is a novel ensemble learning method of human protein-protein interaction prediction via classifier fusion using protein localization information.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • JRE

:: DOWNLOAD

 LocFuse

:: MORE INFORMATION

Citation

LocFuse: human protein-protein interaction prediction via classifier fusion using protein localization information.
Zahiri J, Mohammad-Noori M, Ebrahimpour R, Saadat S, Bozorgmehr JH, Goldberg T, Masoudi-Nejad A.
Genomics. 2014 Dec;104(6 Pt B):496-503. doi: 10.1016/j.ygeno.2014.10.006.

ENTPRISE – Predicting Human Disease-associated Amino Acid Mutations

ENTPRISE

:: DESCRIPTION

ENTPRISE is an algorithm for predicting human disease-associated amino acid mutations from sequence entropy and predicted protein structures

::DEVELOPER

Center for the Study of Systems Biology

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures.
Zhou H, Gao M, Skolnick J.
PLoS One. 2016 Mar 16;11(3):e0150965. doi: 10.1371/journal.pone.0150965.

tfbs_species 1.0 – Map Human Transcription Factor Binding Sites to Another Species

tfbs_species 1.0

:: DESCRIPTION

The aim of tfbs_species is to translate a list of binding sites from the University of California Santa Cruz(UCSC) Genome database from one species to another. At the moment, this data only exists for the human genome

::DEVELOPER

Raymond Wan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

  tfbs_species

:: MORE INFORMATION

MORPHIN – Model Organisms Projected on a Human Integrated Gene Network

MORPHIN

:: DESCRIPTION

MORPHIN is a web-based bioinformatics tool to study human diseases using model organism genes.

::DEVELOPER

Lee Lab at Yonsei University, Korea and the Marcotte Lab at University of Texas at Austin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network.
Hwang S, Kim E, Yang S, Marcotte EM, Lee I.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W147-53. doi: 10.1093/nar/gku434.

LocusExplorer 0.4 – Visualisation of Human Genetic Association data and Biological Annotations

LocusExplorer 0.4

:: DESCRIPTION

LocusExplorer is a data visualisation and exploration tool for genetic association data.

::DEVELOPER

The Oncogenetics Team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 LocusExplorer

:: MORE INFORMATION

Citation

LocusExplorer: a user-friendly tool for integrated visualisation of human genetic association data and biological annotations.
Dadaev T, Leongamornlert DA, Saunders EJ, Eeles R, Kote-Jarai Z.
Bioinformatics. 2015 Nov 20. pii: btv690.

HIPPIE 1.7 – study and filter the Network of Human Protein-protein Interaction data

HIPPIE 1.7

:: DESCRIPTION

HIPPIE (Human Integrated Protein-Protein Interaction rEference) is a human PPI dataset with a normalized scoring scheme that integrates multiple experimental PPI datasets.

::DEVELOPER

Computational Biology and Data Mining Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 HIPPIE

:: MORE INFORMATION

Citation

PLoS One. 2012;7(2):e31826. doi: 10.1371/journal.pone.0031826. Epub 2012 Feb 14.
HIPPIE: Integrating protein interaction networks with experiment based quality scores.
Schaefer MH1, Fontaine JF, Vinayagam A, Porras P, Wanker EE, Andrade-Navarro MA.