dREG – Detection of Regulatory DNA Sequences using GRO-seq Data

dREG

:: DESCRIPTION

dREG is a software for detection of active regulatory elements (promoters & enhancers) using GRO-seq and PRO-seq data.

::DEVELOPER

Danko Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • R

:: DOWNLOAD

 dREG

:: MORE INFORMATION

Citation

Nat Methods. 2015 Mar 23. doi: 10.1038/nmeth.3329.
Identification of active transcriptional regulatory elements from GRO-seq data.
Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, Siepel A

FadE 0.0.2 – DNA Methylation Detection

FadE 0.0.2

:: DESCRIPTION

FadE is a software package which was designed to determine the methylation parameter at each cytosine or cytosine-guanine position in the human genome. FadE uses color reads produced by the SOLiD sequencer.

::DEVELOPER

Ting Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 FadE

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jan 7;41(1):e14. doi: 10.1093/nar/gks830. Epub 2012 Sep 10.
FadE: whole genome methylation analysis for multiple sequencing platforms.
Souaiaia T1, Zhang Z, Chen T.

Proteinortho 6.30 – Orthology Detection Tool

Proteinortho 6.30

:: DESCRIPTION

Proteinortho predicts (co-)orthologous proteins within different species.

::DEVELOPER

Bioinformatics Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Proteinortho

:: MORE INFORMATION

Citation

Lechner et al (2011).
Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis.
BMC Bioinformatics 2011 Apr 28;12(1):124.

Pindel 0.2.5b8 – INDEL (insertions and deletions) Detection

Pindel 0.2.5b8

:: DESCRIPTION

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

::DEVELOPER

The Genome Institute at Washington University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 Pindel

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Nov 1;25(21):2865-71. Epub 2009 Jun 26.
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
Ye K, Schulz MH, Long Q, Apweiler R, Ning Z.

FiToM / xFITOM / jFITOM 201605 – Detection of Binding Sites in DNA or RNA Sequences

FiToM / xFITOM / jFITOM 201605

:: DESCRIPTION

FITOM is a computer program for the detection of binding sites in DNA or RNA sequences. It implements several methods described in the literature to compute an approximation of binding affinity for a particular site based on a collection of binding sequences provided by the user.

xFITOM is a fully featured GUI-enabled version of FITOM for Ms-Windows platforms that integrates additional functionality. The program provides an easy to use graphical user interface (GUI) to define all the relevant options for locating binding sites in genetic sequences.

jFITOM is a Java version of FITOM.

::DEVELOPER

the Erill Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

FITOM , xFITOM , jFITOM

:: MORE INFORMATION

Citation

Erill, I; O’Neill, M.C.
A reexamination of information theory-based methods for DNA-binding site identification
BMC Bioinformatics. 2009 Feb 11;10(1):57

Bhargava, N. & Erill, I. (2010)
xFITOM: a generic GUI tool to search for transcription factor binding sites”,
Bioinformation 5(2) 49-51

ARAGORN 1.2.41 – tRNA (and tmRNA) Detection

ARAGORN 1.2.41

:: DESCRIPTION

ARAGORN is a program to detect tRNA genes and tmRNA genes in nucleotide sequences

::DEVELOPER

ARAGORN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ARAGORN

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2004 Jan 2;32(1):11-6. Print 2004.
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.
Laslett D1, Canback B.

ONCOCNV 6.9 – Detection of Copy Number Changes in Deep Sequencing data

ONCOCNV 6.9

:: DESCRIPTION

ONCOCNV is a package to detect copy number changes in Deep Sequencing data developed by OncoDNA

::DEVELOPER

Boeva lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • R
  • Perl
  • SAMtools

:: DOWNLOAD

 ONCOCNV

:: MORE INFORMATION

Citation

Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data.
Boeva V, Popova T, Lienard M, Toffoli S, Kamal M, Le Tourneau C, Gentien D, Servant N, Gestraud P, Frio TR, Hupé P, Barillot E, Laes JF.
Bioinformatics. 2014 Jul 12. pii: btu436.

VirTect – Detection of Viruses from RNA-Seq on human samples

VirTect

:: DESCRIPTION

VirTect is a computational tool that can use to detect virus from RNA-Seq on human samples.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

VirTect

:: MORE INFORMATION

Citation

Khan A, Liu Q, Chen X, Stucky A, Sedghizadeh PP, Adelpour D, Zhang X, Wang K, Zhong JF.
Detection of human papillomavirus in cases of head and neck squamous cell carcinoma by RNA-seq and VirTect.
Mol Oncol. 2019 Apr;13(4):829-839. doi: 10.1002/1878-0261.12435. Epub 2019 Feb 23. PMID: 30597724; PMCID: PMC6441885.

DeepMod v0.1.3 – Deep-learning tool for DNA Methylation Detection on Nanopore data

DeepMod v0.1.3

:: DESCRIPTION

DeepMod is a computational tool which takes long-read signals as input and outputs modification summary for each genomic position in a reference genome together with modification prediction for each base in a long read.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DeepMod

:: MORE INFORMATION

Citation

Liu Q, Fang L, Yu G, Wang D, Xiao CL, Wang K.
Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data.
Nat Commun. 2019 Jun 4;10(1):2449. doi: 10.1038/s41467-019-10168-2. PMID: 31164644; PMCID: PMC6547721.

LinkedSV – SV Detection on linked-read Sequencing data

LinkedSV

:: DESCRIPTION

LinkedSV is a novel structural variant caller for 10X Genomics (linked-read) sequencing data. It detects deletions, duplications, inversions and translocations using evidence from the barcoded reads.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

LinkedSV

:: MORE INFORMATION

Citation

Fang L, Kao C, Gonzalez MV, Mafra FA, Pellegrino da Silva R, Li M, Wenzel SS, Wimmer K, Hakonarson H, Wang K.
LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data.
Nat Commun. 2019 Dec 6;10(1):5585. doi: 10.1038/s41467-019-13397-7. PMID: 31811119; PMCID: PMC6898185.