PLEK 1.2 – Predictor of Long Non-coding RNAs and mRNAs based on K-mer Scheme

PLEK 1.2

:: DESCRIPTION

PLEK uses an improved computational pipeline based on k-mer and support vector machine (SVM) to distinguish long non-coding RNAs (lncRNAs) from messager RNAs (mRNAs).

::DEVELOPER

PLEK team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C/C++ compiler
Python

:: DOWNLOAD

PLEK

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014 Sep 19;15:311. doi: 10.1186/1471-2105-15-311.
PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme.
Li A, Zhang J1, Zhou Z..

CASPER 0.8.2 – Context-Aware Scheme for Paired-End Read

CASPER 0.8.2

:: DESCRIPTION

CASPER is a state-of-the art merging tool in terms of accuracy and robustness. Using this sophisticated merging method, we could get elongated reads from the forward and reverse reads.

::DEVELOPER

Data Science Laboratory, Seoul National University.

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux

:: DOWNLOAD

CASPER

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014;15 Suppl 9:S10. doi: 10.1186/1471-2105-15-S9-S10. Epub 2014 Sep 10.
CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing.
Kwon S, Lee B, Yoon S.

iDoComp 1.2 – Compression Scheme for Assembled Genomes

iDoComp 1.2

:: DESCRIPTION

iDoComp is an algorithm to compress re-sequenced assembled genomes, i.e., genomes for which an assembled genome of the same species already exists

::DEVELOPER

Mikel Hernaez

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux
C Compiler

:: DOWNLOAD

iDoComp

:: MORE INFORMATION

Citation

iDoComp: A Compression Scheme for Assembled Genomes.
Ochoa I, Hernaez M, Weissman T.
Bioinformatics. 2014 Oct 24. pii: btu698.

HapZipper – Compression Scheme for HapMap Phase III Phased Data

HapZipper

:: DESCRIPTION

HapZipper is a lossless compression tool tailored to compress HapMap data beyond benchmarks defined by generic tools such as gzip, bzip2 and lzma.

::DEVELOPER

Joel Bader lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux / Windows
JRE

:: DOWNLOAD

HapZipper

:: MORE INFORMATION

Citation

HapZipper: sharing HapMap populations just got easier.
Chanda P, Elhaik E, Bader JS.
Nucleic Acids Res. 2012 Nov 1;40(20):e159. doi: 10.1093/nar/gks709.