Tag: Detection

VariationHunter 0.04 – Structural Variation Detection

VariationHunter 0.04

:: DESCRIPTION

VariationHunter-CL (VariationHunter-CommonLaw)is a package of programs need to find structural variations which mappings of paired-end reads are known.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • C Complier

:: DOWNLOAD

 VariationHunter

:: MORE INFORMATION

Citation

Next Generation VariationHunter: Combinatorial Algorithms for Transposon Insertion Discovery
Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yorukoglu, Can Alkan, Evan E. Eichler, S. Cenk Sahinalp
Bioinformatics 2010 Jun 15;26(12):i350-i357

TPpred 3.0 – Detection of Mitochondrial-targeting Signals in Proteins

TPpred 3.0

:: DESCRIPTION

TPpred is a web server for MITOCHONDRIAL targeting peptides prediction in proteins. TPpred is optimized for the prediction of cleavage sites of mitochondrial targeting peptides.

::DEVELOPER

Bologna Biocomputing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • BioPython
  • EMBOSS

:: DOWNLOAD

  TPpred

:: MORE INFORMATION

Citation

TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in Eukaryotic proteins.
Savojardo C, Martelli PL, Fariselli P, Casadio R.
Bioinformatics. 2015 Jun 16. pii: btv367

TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs.
Savojardo C, Martelli PL, Fariselli P, Casadio R.
Bioinformatics. 2014 Jun 27. pii: btu411.

OD-seq 0.99.3 – Outlier Detection in Multiple Sequence Alignments

OD-seq 0.99.3

:: DESCRIPTION

OD-seq is a practical and simple method to detect outliers in MSAs. It can also detect outliers in sets of unaligned sequences, but with reduced accuracy.

::DEVELOPER

Prof. Des Higgins

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 OD-seq

:: MORE INFORMATION

Citation

OD-seq: outlier detection in multiple sequence alignments.
Jehl P, Sievers F, Higgins DG.
BMC Bioinformatics. 2015 Aug 25;16:269. doi: 10.1186/s12859-015-0702-1.

HybridCheck v1.0.1 – Hybridisation Recombination and Introgression Detection and Dating

HybridCheck v1.0.1

:: DESCRIPTION

HybridCheck is a software package to visualise the recombination signal in large DNA sequence dataset, and it can be used to analyse recombination, genetic introgression, hybridisation and horizontal gene transfer.

::DEVELOPER

HybridCheck team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

  HybridCheck

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2015 Sep 23. doi: 10.1111/1755-0998.12469. [Epub ahead of print]
HybridCheck: software for the rapid detection, visualisation and dating of recombinant regions in genome sequence data.
Ward BJ, van Oosterhout C.

rbrothers – Multiple Change-point Recombination Detection

rbrothers

:: DESCRIPTION

R package rbrothers provides easy access to recombination detection software DualBrothers and provides new functionality for pre-processing sequence data and post-processing DualBrothers output.

::DEVELOPER

rbrothers team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

  rbrothers

:: MORE INFORMATION

Citation

Evol Bioinform Online. 2013 Jun 12;9:235-8. doi: 10.4137/EBO.S11945. Print 2013.
rbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection.
Irvahn J1, Chattopadhyay S, Sokurenko EV, Minin VN.

SplicingViewer 1.1.0 – Detection, Annotation and Visualization of the Alternative Splicing from RNA-Seq Data

SplicingViewer 1.1.0

:: DESCRIPTION

SplicingViewer is an integrated tool which can detect the splice junctions based on known gene models, annotate the alternative splicing patterns based on the splice junctions, and visualize the patterns of alternative splicing events. In addition, as a viewer, SplicingViewer can also be used to display the RNA-Seq reads mapping results with high speed and lower memory spend.

::DEVELOPER

SplicingViewer team

:: SCREENSHOTS

SplicingViewer

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 SplicingViewer

:: MORE INFORMATION

Citation

Genomics. 2012 Mar;99(3):178-82. doi: 10.1016/j.ygeno.2011.12.003. Epub 2011 Dec 28.
Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer.
Liu Q, Chen C, Shen E, Zhao F, Sun Z, Wu J.

RNASeqBias 1.0 – Bias Detection and Correction in RNA-Sequencing Data

RNASeqBias 1.0

:: DESCRIPTION

RNASeqBias contains functions and sample data for detecting and correcting for biases in gene expression levels from RNA-Seq experiments. Considered bias factors are gene length, GC content and dinucleotide frequencies. Principal component analysis on GC content and dinucleotide frequencies are first performed, and the resulting principal components and gene length were used as covariates to fit a generalized additive model with smoothing spline on gene expression levels as response. The package also have codes to generate bias plots before and after bias correction, and to compare with other quantitative platforms.

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RNASeqBias

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Jul 19;12:290. doi: 10.1186/1471-2105-12-290.
Bias detection and correction in RNA-Sequencing data.
Zheng W1, Chung LM, Zhao H.

BHIT – SNP Interaction Detection

BHIT

:: DESCRIPTION

BHIT (Bayesian High-order Interaction Toolkit), a novel Bayesian partition computational method for detecting SNP interactions (epistasis).

::DEVELOPER

Digital Biology Laboratory, University Of Missouri-Columbia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BHIT

:: MORE INFORMATION

Citation

Juexin Wang, Jason Kasvin-Felton, Namita Gupta, Mate Nagy, Trupti Joshi, Babu Valliyodan, Haiying Shi, Yanchun Liang, Henry T. Nguyen, Jing Zhang, Dong Xu.
A Bayesian Model for Detection of High-order Interactions among Genetic Variants in Genome-wide Association Studies.
BMC Genomics. 2015 Nov 25;16(1):1011.

RDiff 0.3 – Accurate Detection of Differential RNA Processing

RDiff 0.3

:: DESCRIPTION

rDiff is an open source tool for accurate detection of differential RNA processing from RNA-Seq data. It implements two statistical tests to detect changes of the RNA processing between two samples. rDiff.parametric is a powerful test, which can be applied for well annotated organisms to detect changes in the relative abundance of isoforms. rDiff.nonparametric is an alternative when the annotation is incomplete or missing.

::DEVELOPER

the Biomedical Informatics Lab of Prof. Dr. Gunnar Rätsch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • SAMTools

:: DOWNLOAD

 RDiff 

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 May 1;41(10):5189-98. doi: 10.1093/nar/gkt211. Epub 2013 Apr 12.
Accurate detection of differential RNA processing.
Drewe P, Stegle O, Hartmann L, Kahles A, Bohnert R, Wachter A, Borgwardt K, Rätsch G.

YAHA 0.1.83 – Long-read Alignment with Optimal Breakpoint Detection

YAHA 0.1.83

:: DESCRIPTION

YAHA is a flexible, sensitive and accurate hash-based DNA aligner for relatively long queries that operates in three distinct modes. It can output all the alignments found for each query, only the set of alignments that optimally cover each query, or add alignments that are similar to those that optimally cover the query.

::DEVELOPER

 Greg Faust (gf4ea@virginia.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 YAHA

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Oct 1;28(19):2417-24. Epub 2012 Jul 24.
YAHA: fast and flexible long-read alignment with optimal breakpoint detection.
Faust GG1, Hall IM.