Tag: Human Genome

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

Paed Lab @ 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

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

GenoCanyon

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: 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.

MyGenome 4.0 – Explore Real Human Genome

MyGenome 4.0

:: DESCRIPTION

MyGenome explores a real human genome. Find out about possible health implications. View reports about important genetic variations. The MyGenome app provides a simple, intuitive, and educational interface to get you started on your journey of genome discovery and learning.

::DEVELOPER

Illumina Clinical Services Laboratory

:: SCREENSHOTS

MyGenome

:: REQUIREMENTS

  •  iPad

:: DOWNLOAD

 MyGenome

:: MORE INFORMATION

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

IntSplice

:: 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.

Human Genome 1.0.2 – Obtain information about a known Gene

Human Genome 1.0.2

:: DESCRIPTION

The Human Genome App is designed so that a person can obtain information about a known gene or discover relationships between genes and diseases, syndromes or traits.

::DEVELOPER

Florence Haseltine

:: SCREENSHOTS

HumanGenome

:: REQUIREMENTS

  •  iPad

:: DOWNLOAD

 Human Genome

:: 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.

CS-SCORE – Rapid Identification and Removal of human Genome Contaminants from Metagenomic datasets

CS-SCORE

:: DESCRIPTION

CS-SCORE is a novel algorithm that can rapidly identify (with high sensitivity) host sequences contaminating metagenomic datasets.

::DEVELOPER

CS-SCORE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CS-SCORE

:: MORE INFORMATION

Citation:

CS-SCORE: Rapid identification and removal of human genome contaminants from metagenomic datasets.
Haque MM, Bose T, Dutta A, Reddy CV, Mande SS.
Genomics. 2015 May 2. pii: S0888-7543(15)00075-0. doi: 10.1016/j.ygeno.2015.04.005.

GenomeCache 1.5 – Explore both McMillian Park and the realm of the Human Genome

GenomeCache 1.5

:: 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

CpGIMethPred 1.0 – Predict Methylation Status of CpG Islands in Human Genome

CpGIMethPred 1.0

:: DESCRIPTION

CGIMetPred is a program to predict the methylation status of CpG islands in normal CD4 lymphocytes.

::DEVELOPER

Hao Zheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

 CpGIMethPred

:: MORE INFORMATION

Citation

BMC Med Genomics. 2013;6 Suppl 1:S13. doi: 10.1186/1755-8794-6-S1-S13. Epub 2013 Jan 23.
CpGIMethPred: computational model for predicting methylation status of CpG islands in human genome.
Zheng H1, Wu H, Li J, Jiang SW.

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.