RAT – A software for Rapid Association Tests

RAT

:: DESCRIPTION

RAT (Rapid Association Test) is a software for testing association between single nucleotide polymorphisms (SNPs) and a disease. The main advantage of RAT is its ability to calculate accurately and quickly high significance disease association. For large data set and low p-values, RAT is 2-4 orders of magnitude faster than the standard permutation test.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows with Cygwin /Linux

:: DOWNLOAD

  RAT

:: MORE INFORMATION

Citation

Gad Kimmel and Ron Shamir.
A Fast Method for Computing High Significance Disease Association in Large Population-Based Studies.
Am. J. Hum. Genet. 2006

SpeedSeq v0.1.2 – Framework for Rapid Genome Analysis and Interpretation

SpeedSeq v0.1.2

:: DESCRIPTION

SpeedSeq is an open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SpeedSeq

:: MORE INFORMATION

Citation:

Nat Methods. 2015 Oct;12(10):966-8. doi: 10.1038/nmeth.3505. Epub 2015 Aug 10.
SpeedSeq: ultra-fast personal genome analysis and interpretation.
C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall.

RaPID 1.7 – Random Projection-based IBD Detection

RaPID 1.7

:: DESCRIPTION

RaPID is a software of ultra-fast identity by descent (IBD) detection in large cohorts using positional Burrows-Wheeler transform

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

RaPID

:: MORE INFORMATION

Citation

RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts.
Naseri A, Liu X, Tang K, Zhang S, Zhi D.
Genome Biol. 2019 Jul 25;20(1):143. doi: 10.1186/s13059-019-1754-8.

PARALIGN 5.0 – Rapid and Sensitive Sequence Similarity Searches

PARALIGN 5.0

:: DESCRIPTION

PARALIGN is a sequence database search application based on local sequence alignments. It incorporates the most sensitive algorithms for searching sequence databases based on local sequence alignments. Implementation of these algorithms at a very high speed has been achieved by exploiting the advanced parallel processing technology embedded in modern microprocessors.

:: DEVELOPER

 Sencel Bioinformatics. 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 PARALIGN

:: MORE INFORMATION

Citation:

Sæbø PE, Andersen SM, Myrseth J, Laerdahl JK, Rognes T (2005)
PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology.
Nucleic Acids Research, 33 (Suppl 2), W535-W538.

RAPID – Regression-based Accurate Prediction of protein Intrinsic Disorder Content

RAPID

:: DESCRIPTION

RAPID is a server providing fast and accurate sequence based prediction of protein disorder content.

::DEVELOPER

Kurgan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Biochim Biophys Acta. 2013 Aug;1834(8):1671-80. doi: 10.1016/j.bbapap.2013.05.022. Epub 2013 Jun 1.
RAPID: fast and accurate sequence-based prediction of intrinsic disorder content on proteomic scale.
Yan J1, Mizianty MJ, Filipow PL, Uversky VN, Kurgan L.

PATHGROUPS – Rapid Small Phylogeny

PATHGROUPS

:: DESCRIPTION

The PATHGROUPS program optimizes the gene order at ancestral nodes of a given phylogeny, given the order in modern genomes.

::DEVELOPER

Sankoff Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 PATHGROUPS

:: MORE INFORMATION

Citaion

On the PATHGROUPS approach to rapid small phylogeny.
Zheng C, Sankoff D.
BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S4.

RADAR 1.1.5 – Rapid Automatic Detection and Alignment of Repeats in protein sequences

RADAR 1.1.5

:: DESCRIPTION

RADAR identifies gapped approximate repeats and complex repeat architectures involving many different types of repeats.

::DEVELOPER

European Bioinformatics Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • Python

:: DOWNLOAD

  RADAR

:: MORE INFORMATION

Citation:

Rapid automatic detection and alignment of repeats in protein sequences. (2000)
Heger A. and Holm L.
Proteins 41(2): 224-237.