Bioclojure – Functional Library for the Manipulation of Biological Sequences

Bioclojure

:: DESCRIPTION

BioClojure is an open-source library for the manipulation of biological sequence data written in the language Clojure. BioClojure aims to provide a functional framework for the processing of biological sequence data that provides simple mechanisms for concurrency and lazy evaluation of large datasets.

::DEVELOPER

Bioclojure team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
Java

:: DOWNLOAD

BioClojure

:: MORE INFORMATION

Citation

Bioclojure: a functional library for the manipulation of biological sequences.
Plieskatt J, Rinaldi G, Brindley PJ, Jia X, Potriquet J, Bethony J, Mulvenna J.
Bioinformatics. 2014 May 2. pii: btu311

scrm 1.7.4 – Coalescent Simulator for Biological Sequences

scrm 1.7.4

:: DESCRIPTION

scrm (sequential coalescent with recombination model ) is a coalescent simulator for biological sequences. Different to similar programs, it can approximate the Ancestral Recombination Graph as closely as needed, but still has only linear runtime cost for long sequences. It allows you to rapidly simulate chromosome scale sequences with essentially correct genetic linkage.

::DEVELOPER

scrm team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX

:: DOWNLOAD

scrm

:: MORE INFORMATION

Citation

scrm: efficiently simulating long sequences using the approximated coalescent with recombination.
Staab PR, Zhu S, Metzler D, Lunter G.
Bioinformatics. 2015 Jan 8. pii: btu861

Teiresias 0.9.1 – Combinatorial Pattern Discovery in Biological Sequences

Teiresias 0.9.1

:: DESCRIPTION

The Teiresias algorithm is a combinatorial algorithm for the discovery of rigid patterns (motifs) in biological sequences.

::DEVELOPER

the Computational Medicine Center at the Sidney Kimmel Medical College of Thomas Jefferson University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX

:: DOWNLOAD

Teiresias

:: MORE INFORMATION

Tutorial for online or local use

Wikipedia page

Citation:

Bioinformatics. 1998;14(1):55-67.
Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm.
Rigoutsos I1, Floratos A.

PANOW 1.0 – Search of Rare Words in Biological Sequences

PANOW 1.0

:: DESCRIPTION

PANOW (Poisson Approximation for the Number of Occurrences of Words)is a software dedicated to the search of rare words in biological sequences (over- or under-represented words in DNA or protein sequences).

::DEVELOPER

Nicolas Vergne (vergne@genopole.cnrs.fr)@ Laboratoire de Mathématiques et Modélisation d’Évry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX
seq++
C++ Compiler

:: DOWNLOAD

PANOW

:: MORE INFORMATION

Citation

N. Vergne and M. Abadi.
Poisson approximation for search of rare words in DNA sequences,
ALEA Vol. 4 pp. 223-244, 2008.

Sirius PSB 2.3.3 – Generic System for Analysis of Biological Sequences

Sirius PSB 2.3.3

:: DESCRIPTION

Sirius PSB (Sirius Prediction System Builder) is a software to carry out sequence (DNA or protein) analysis. Main operations: 1) Building a classifier 2) Deploying a classifer 3) Search for proteins similar to query proteins 4) Preliminary and post prediction analysis (Visualization)

::DEVELOPER

Sirius PSB Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOsX
Java

:: DOWNLOAD

Sirius PSB

:: MORE INFORMATION

Citation:

Koh CH, Lin S, Jedd G, Wong L:
Sirius PSB: A Generic System for Analysis of Biological Sequences.
Journal of Bioinformatics and Computational Biology, 7(6): 973-990, December 2009.