OligoCalc 3.26 – Oligonucleotide Properties Calculator

OligoCalc 3.26

:: DESCRIPTION

OligoCalc is a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intra-molecular hairpin loop formation.

::DEVELOPER

Warren A. Kibbe, Ph.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 OligoCalc

:: MORE INFORMATION

Citation

Kibbe WA.
OligoCalc: an online oligonucleotide properties calculator‘. (2007)
Nucleic Acids Res. 35(webserver issue): May 25.

RaptorX Property 1.02 – Protein Structure Property Prediction

RaptorX Property 1.02

:: DESCRIPTION

RaptorX Property is a web server predicting structure property of a protein sequence without using any template information.

::DEVELOPER

Xu group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

PRaptorX Property

:: MORE INFORMATION

Citation:

RaptorX-Property: a web server for protein structure property prediction.
Wang S, Li W, Liu S, Xu J.
Nucleic Acids Res. 2016 Apr 25. pii: gkw306.

GraPPLE – Graph Property based Predictor and Likelihood Estimator

GraPPLE

:: DESCRIPTION

GraPPLE are abstract representations of relationships between entities. Through a set of instructions, they are able to convert relationships into nodes and edges. GraPPLE (originally: The RNA sorting hat) leverages the information available from graph properties and the predictive power of support vector machines (SVMs) to classify potential RNA sequences as functional/non-functional and into 1 of 46 Rfam families. In short, GraPPLE predicts the potential function of an ncRNA sequence.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 May;37(9):e66. Epub 2009 Apr 1.
Identification and classification of ncRNA molecules using graph properties.
Childs L, Nikoloski Z, May P, Walther D.

TreeSAAP 3.2 – Selection of Amino Acid Properties using Phylogenetic Trees model

TreeSAAP 3.2

:: DESCRIPTION

TreeSAAP (Selection of Amino Acid Properties Based on Phylogenetic Trees) measures the selective influences on 31 structural and biochemical amino acid properties during phylogenesis (the history of genealogical development) and performs goodness-of-fit and categorical statistical tests.

::DEVELOPER

McClellan, David

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

TreeSAAP

:: MORE INFORMATION

Citation

TreeSAAP: selection on amino acid properties using phylogenetic trees.
Woolley S, Johnson J, Smith MJ, Crandall KA, McClellan DA.
Bioinformatics. 2003 Mar 22;19(5):671-2

PHYSICO 2 – Computation of Properties of Protein Sequences

PHYSICO 2

:: DESCRIPTION

PHYSICO2 is an UNIX based Standalone Procedure for Computation of Physicochemical, Window-dependent and Substitution Based Evolutionary Properties of Protein Sequences along with Automated Block Preparation Tools.

::DEVELOPER

PHYSICO team

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PHYSICO

:: MORE INFORMATION

Citation:

PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2.
Banerjee S, Gupta PS, Nayek A, Das S, Sur VP, Seth P, Islam RN, Bandyopadhyay AK.
Bioinformation. 2015 Jul 31;11(7):366-8. doi: 10.6026/97320630011366.