D2Z 0.1 – Alignment Free Comparison of Regulatory Sequences

D2Z 0.1

:: DESCRIPTION

D2Z is based on comparing the frequencies of all fixed-length words in the two sequences. An important, novel feature of the score is that it is comparable across sequence pairs drawn from arbitrary background distributions.

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
GCC

:: DOWNLOAD

D2Z Source Code

:: MORE INFORMATION

Citation:

A statistical method for alignment-free comparison of regulatory sequences
Miriam R. Kantorovitz,Gene E. Robinson, Saurabh Sinha.
Bioinformatics. 2007 Jul 1;23(13):i249-55.

gkm-SVM 2.0 – Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

gkm-SVM 2.0

:: DESCRIPTION

gkm-SVM is a new classifier and a general method for robust estimation of k-mer frequencies.

::DEVELOPER

BeerLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux
C++ COmpiler

:: DOWNLOAD

gkm-SVM

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2014 Jul 17;10(7):e1003711. doi: 10.1371/journal.pcbi.1003711. eCollection 2014.
Enhanced regulatory sequence prediction using gapped k-mer features.
Ghandi M, Lee D, Mohammad-Noori M, Beer MA