Tag: Human Genome

iDHS-EL – Identifying the location of DHS in human Genome

iDHS-EL

:: DESCRIPTION

iDHS-EL is a webserver of identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Liu B, Long R, Chou KC.
iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework.
Bioinformatics. 2016 Aug 15;32(16):2411-8. doi: 10.1093/bioinformatics/btw186. Epub 2016 Apr 8. PMID: 27153623.

GenomeCache 2.0.1 – Explore both McMillian Park and the realm of the Human Genome

GenomeCache 2.0.1

:: DESCRIPTION

Genome Cache  was developed by the Educational Outreach Team at the HudsonAlpha Institute for Biotechnology in Huntsville, Alabama. The original Genome Walk was created for McMillian Park, an outdoor area on the HudsonAlpha campus. The goal of Genome Cache? was to provide an engaging way for students and the public to explore both McMillian Park and the realm of the human genome.

::DEVELOPER

HudsonAlpha Institute for Biotechnology

:: SCREENSHOTS

GenomeCache

:: REQUIREMENTS

  •  iPad / iPhone

:: DOWNLOAD

 GenomeCache

:: MORE INFORMATION

DNN-HMM – De novo Identification of Replication-timing Domains in the Human Genome

DNN-HMM

:: DESCRIPTION

DNN-HMM (deep neural network and a hidden Markov model) is a novel hybrid architecture combining a pre-trained,for the de novo identification of replication domains using replication timing profiles.

::DEVELOPER

DNN-HMM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab / Perl

:: DOWNLOAD

  DNN-HMM

:: MORE INFORMATION

Citation

De novo Identification of replication-timing domains in the human genome by deep learning.
Liu F, Ren C, Li H, Zhou P, Bo X, Shu W.
Bioinformatics. 2015 Nov 5. pii: btv643.

GenoCanyon 1.0.3 – Predict Functional Non-coding Regions in Human Genome

GenoCanyon 1.0.3

:: DESCRIPTION

GenoCanyon is a whole-genome functional annotation approach based on unsupervised statistical learning.

::DEVELOPER

Hongyu Zhao’s Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

GenoCanyon

:: MORE INFORMATION

Citation

A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data.
Lu Q, Hu Y, Sun J, Cheng Y, Cheung KH, Zhao H.
Sci Rep. 2015 May 27;5:10576. doi: 10.1038/srep10576.

Haplotter – Explore the Evidence for Recent Positive Selection in the Human Genome

Haplotter

:: DESCRIPTION

Haplotter is a web application that has been developed to display the results of a scan for positive selection in the human genome using the HapMap data.

::DEVELOPER

Pritchard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS Biol. 2006 Mar;4(3):e72. Epub 2006 Mar 7.
A map of recent positive selection in the human genome.
Voight BF1, Kudaravalli S, Wen X, Pritchard JK.

IntSplice 1.1 – Prediction of the Splicing Consequences of Intronic Single-nucleotide Variations in the Human Genome

IntSplice 1.1

:: DESCRIPTION

IntSplice is a tool to predict a splicing consequence of an SNV at intron positions -50 to -3 close the 3’ end of an intron of the human genome.

::DEVELOPER

IntSplice team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

IntSplice: prediction of the splicing consequences of intronic single-nucleotide variations in the human genome.
Shibata A, Okuno T, Rahman MA, Azuma Y, Takeda JI, Masuda A, Selcen D, Engel AG, Ohno K.
J Hum Genet. 2016 Mar 24. doi: 10.1038/jhg.2016.23.

SRinversion – Detection of Short Inversions in Human Genome using Next Generation Sequencing Data

SRinversion

:: DESCRIPTION

SRinversion is a framework to analyze poorly mapped or unmapped reads by splitting and re-aligning them for the purpose of inversion detection.

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICS @ University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
  • Perl

:: DOWNLOAD

 SRinversion

:: MORE INFORMATION

Citation

SRinversion: a tool for detecting short inversions by splitting and re-aligning poorly mapped and unmapped sequencing reads.
Chen R, Lau YL, Zhang Y, Yang W.
Bioinformatics. 2016 Aug 8. pii: btw516

Nature Human Genome Special Edition 1.0

Nature Human Genome Special Edition 1.0

:: DESCRIPTION

The Nature Human Genome iPad special edition contains landmark research as well as exclusive video commentary from Nature’s genetics editor, who discusses the past, present and future of genomics. In addition, the App features an interactive graph displaying a timeline of human genome research over the past ten years and includes audio clips from authors discussing their papers.

::DEVELOPER

Nature Publishing Group

:: SCREENSHOTS

:: REQUIREMENTS

  •  iPad

:: DOWNLOAD

 Nature Human Genome iPad special edition

:: MORE INFORMATION

RTanalyzer – Searche for Retro-transposition Elements in the Human Genome

RTanalyzer

:: DESCRIPTION

RTAnalyzer looks for a target site duplication, a polyA in 3′ and an endonuclease cleavage site in 5′ to calculate an overall score of retrotransposition.RTanalyzer will be useful for indepth analysis of non-autonomous retrotransposons in sequenced mammals to help us understand retrotransosition in our evolutionary tree.

::DEVELOPER

RiboClub

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RTanalyzer

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W269-74. Epub 2007 Jun 1.
RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures.
Lucier JF, Perreault J, No?l JF, Boire G, Perreault JP.

 

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