Dragon TIS Spotter 1.1 – Search for Translation Initiation Sites (TISs) in Arabidopsis Genomic Sequences

Dragon TIS Spotter 1.1

:: DESCRIPTION

Dragon TIS Spotter (DTS) searches for Translation Initiation Sites (TISs) in Arabidopsis genomic sequences provided in fasta sequence format. The program analyzes contend of the sliding windows of 300 bp of DNA sequence, assuming the TIS is located at 150-152 position of the window counted from the 5′ end.

::DEVELOPER

Dragon TIS Spotter Team @ Computational Bioscience Research Center , King Abdullah University of Science and Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Dragon TIS Spotter

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Oct 30.
Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants.
Mora AM, Ashoor H, Jankovic BR, Kamau A, Awara K, Chowdhary R, Archer JA, Bajic VB.

STAR – Search for Tandem Approximate Repeats

STAR

:: DESCRIPTION

The program STAR (Search for Tandem Approximate Repeats) searches for significant Approximate Tandem Repeats (ATR) of a given motif in a DNA sequence. For each region of the sequence that is similar to a tandem repeat of the input motif, STAR returns a description of the segment that it calls a “Zone”, and an optimal alignment of the zone with the best possible Exact Tandem Repeat. (Here, exact means perfect.) STAR optimally detects all such zones in the sequence.

::DEVELOPER

Olivier Delgrange , Eric Rivals

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX

:: DOWNLOAD

STAR

:: MORE INFORMATION

Citation

“STAR: an algorithm to Search for Tandem Approximate Repeats.”
Delgrange O. and Rivals E.
Bioinformatics. 2004 20(16):2812-2820.

RNAplex 0.2 – Search for Short Interactions between two long RNAs

RNAplex 0.2

:: DESCRIPTION

RNAplex is a tool especially created to rapidly search for short interactions between two long RNAs.

::DEVELOPER

Hakim Tafer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX
Perl

:: DOWNLOAD

RNAplex

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Nov 15;24(22):2657-63. Epub 2008 Apr 23.
RNAplex: a fast tool for RNA-RNA interaction search.
Tafer H, Hofacker IL.