ezVIR 2 – Human Virus Screening from high-throughput Sequencing data

ezVIR 2

:: DESCRIPTION

ezVIR is a bioinformatics pipeline which was designed to process HTS data from any of the standard platforms and to evaluate the entire spectrum of known human viruses at once, providing results that are easy to interpret and customizable.

::DEVELOPER

Prof Zdobnov Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

ezVIR

:: MORE INFORMATION

Citation

Petty TJ, Cordey S, Padioleau I, Docquier M, Turin L, Preynat-Seauve O, Zdobnov EM, Kaiser L.
Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study.
J Clin Microbiol. 2014 Sep;52(9):3351-61. doi: 10.1128/JCM.01389-14. Epub 2014 Jul 9. PMID: 25009045; PMCID: PMC4313162.

CisRNA-SVM – Identification of Structured Cis-regulatory Elements in the 3’UTRs of human Protein-coding mRNAs

CisRNA-SVM

:: DESCRIPTION

CisRNA-SVM is a software for genome wide predictions of novel structured RNA cis-regulatory elements in human 3′ UTRs.

::DEVELOPER

Dr Chris Brown’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux
Perl

:: DOWNLOAD

CisRNA-SVM

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Oct;40(18):8862-73. doi: 10.1093/nar/gks684. Epub 2012 Jul 20.
Computational identification of new structured cis-regulatory elements in the 3′-untranslated region of human protein coding genes.
Chen XS1, Brown CM.

microDoR – Prediction of Human miRNA-Mediated Gene Silencing

microDoR

:: DESCRIPTION

microDoR Human is an online machine learning algorithm based on SVM (support vector machine) to predict Human miRNA-mediated gene silencing: mRNA degradation or translational repression, and it can also determine whether a mRNA is a target of a miRNA according to Pictar and PITA.

::DEVELOPER

microDoR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Comput Biol Med. 2012 Jan;42(1):1-7. doi: 10.1016/j.compbiomed.2011.10.001.
Predicting miRNA-mediated gene silencing mode based on miRNA-target duplex features.
Song X1, Cheng L, Zhou T, Guo X, Zhang X, Chen YP, Han P, Sha J.

Epigram 0.004 – Predicting Human Epigenome from DNA Motifs

Epigram 0.004

:: DESCRIPTION

Epigram is an analysis pipeline that predicts histone modification and DNA methylation patterns from DNA motifs.

::DEVELOPER

Wei Wang’s group

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux

:: DOWNLOAD

Epigram

:: MORE INFORMATION

Citation

Nat Methods. 2015 Mar;12(3):265-72. doi: 10.1038/nmeth.3065. Epub 2014 Sep 21.
Predicting the human epigenome from DNA motifs.
Whitaker JW, Chen Z, Wang W

funtooNorm 1.00.1 – Normalization of Illumina Infinium Human Methylation 450 BeadChip

funtooNorm 1.00.1

:: DESCRIPTION

The R package funtooNorm provides a function for normalization of Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K) data when there are samples from multiple tissues or cell types.

::DEVELOPER

Greenwood Lab, Statistical Genetics at the Lady Davis Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux/ MacOSX
R

:: DOWNLOAD

funtooNorm

:: MORE INFORMATION

Citation

funtooNorm: an R package for normalization of DNA methylation data when there are multiple cell or tissue types.
Oros Klein K, Grinek S, Bernatsky S, Bouchard L, Ciampi A, Colmegna I, Fortin JP, Gao L, Hivert MF, Hudson M, Kobor MS, Labbe A, MacIsaac JL, Meaney MJ, Morin AM, O’Donnell KJ, Pastinen T, Van Ijzendoorn MH, Voisin G, Greenwood CM.
Bioinformatics. 2015 Oct 24. pii: btv615.

TAM 2.0 – Annotations of meaningful human miRNAs Categories

TAM 2.0

:: DESCRIPTION

TAM (The tool for annotations of human miRNAs) integrated miRNAs into different sets according to various rules and provides investigators with functions to mine potential biological meaning behind list of interested miRNAs.

TAM 2.0 is the updated web server of our previously published miRNA set enrichment analysis tool,

::DEVELOPER

the Cui Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

TAM

:: MORE INFORMATION

Citation

Li J, Han X, Wan Y, Zhang S, Zhao Y, Fan R, Cui Q, Zhou Y.
TAM 2.0: tool for MicroRNA set analysis.
Nucleic Acids Res. 2018 Jul 2;46(W1):W180-W185. doi: 10.1093/nar/gky509. PMID: 29878154; PMCID: PMC6031048.

BMC Bioinformatics. 2010 Aug 9;11:419. doi: 10.1186/1471-2105-11-419.
TAM: a method for enrichment and depletion analysis of a microRNA category in a list of microRNAs.
Lu M1, Shi B, Wang J, Cao Q, Cui Q.

ENTPRISE / ENTPRISE-X – Predicting Human Disease-associated Amino Acid Mutations

ENTPRISE / ENTPRISE-X

:: DESCRIPTION

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

ENTPRISE-X is an algorithm for predicting human disease-associated frameshift & nonsense mutations.

::DEVELOPER

Center for the Study of Systems Biology

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: 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.

Zhou H, Gao M, Skolnick J.
ENTPRISE-X: Predicting disease-associated frameshift and nonsense mutations.
PLoS One. 2018 May 3;13(5):e0196849. doi: 10.1371/journal.pone.0196849. PMID: 29723276; PMCID: PMC5933770.

VarioBox 1.4.6 – Exploring Human Genetic Variations

Variobox 1.4.6

:: DESCRIPTION

Variobox is a desktop tool for the annotation, analysis and comparison of human genes. Variant annotation data are obtained from WAVe, protein metadata annotations are gathered from PDB and UniProt, and sequence metadata is obtained from Locus Reference Genomic (LRG) and RefSeq databases.

::DEVELOPER

UA.PT Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux/ MacOsX
Java

:: DOWNLOAD

VarioBox

:: MORE INFORMATION

Citation

Hum Mutat. 2014 Feb;35(2):202-7. doi: 10.1002/humu.22474. Epub 2013 Nov 21.
Variobox: automatic detection and annotation of human genetic variants.
Gaspar P1, Lopes P, Oliveira J, Santos R, Dalgleish R, Oliveira JL.

WebSTR – Population-wide database of short Tandem Repeat Variation in humans

WebSTR

:: DESCRIPTION

WebSTR is a web application for browsing a variety of STR datasets. It is based off of the popular ExAC browser.

::DEVELOPER

Gymrek Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

MetaQuery 1.0.4 – Annotation and Quantitative analysis of Genes in the human Gut Microbiome

MetaQuery 1.0.4

:: DESCRIPTION

MetaQuery is a web application for rapid and quantitative analysis of specific genes in the human gut microbiome.

::DEVELOPER

Pollard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

MetaQuery

:: MORE INFORMATION

Citation

MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome.
Nayfach S, Fischbach MA, Pollard KS.
Bioinformatics. 2015 Jun 22. pii: btv382.