Tag: Lightweight

CONUS 1.0 – Exploration of Lightweight Stochastic Context Free Grammars

CONUS 1.0

:: DESCRIPTION

CONUS is an implementation of simple stochastic context-free grammars for RNA secondary structure analysis.CONUS developed for exploring the consequences of different single sequence SCFG designs in predicting RNA secondary structure.

::DEVELOPER

Eddy lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CONUS

:: MORE INFORMATION

Citation

Dowell, RD and Eddy, SR.
Evaluation of Several Lightweight Stochastic Context Free Grammars for RNA Secondary Structure Prediction.
BMC Bioinformatics 5:71 (2004).

LightAssembler – Lightweight Resources Assembly Algorithm

LightAssembler

:: DESCRIPTION

LightAssembler is a lightweight assembly algorithm designed to be executed on a desktop machine. It uses a pair of cache oblivious Bloom filters, one holding a uniform sample of g-spaced sequenced k-mers and the other holding k-mers classified as likely correct, using a simple statistical test.

::DEVELOPER

Sara El-Metwally

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LightAssembler

:: MORE INFORMATION

Citation

LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads.
El-Metwally S, Zakaria M, Hamza T.
Bioinformatics. 2016 Jul 13. pii: btw470.