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

:: 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.

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.