Tag: Calculator

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.

MGEnrichment – Microglia Gene List Enrichment Calculator

MGEnrichment

:: DESCRIPTION

MGEnrichment is a web application developed both to disseminate to the community our curated database of microglia-relevant gene lists, and to allow non-programming scientists to easily conduct statistical enrichment analysis on their gene expression data.

::DEVELOPER

Ciernia Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web server

:: DOWNLOAD

MGEnrichment

:: MORE INFORMATION

Citation

Jao J, Ciernia AV.
MGEnrichment: A web application for microglia gene list enrichment analysis.
PLoS Comput Biol. 2021 Nov 17;17(11):e1009160. doi: 10.1371/journal.pcbi.1009160. PMID: 34788279; PMCID: PMC8598070.

nuScore – DNA Deformation Energy and Nucleosome-positioning Score Calculator

nuScore

:: DESCRIPTION

nuScore allows estimation of the affinity of the histone core to DNA and prediction of nucleosome arrangement on a given sequence. The algorithm is based on assessment of the energy cost of imposing the deformations required to wrap DNA around the histone surface

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Tolstorukov MY, Choudhary V, Olson WK, Zhurkin VB, Park PJ.
nuScore: a web-interface for nucleosome positioning predictions.
Bioinformatics. 2008. 24:1456-1458.

IDCalc 0.3 – Isotope Distribution Calculator

IDCalc 0.3

:: DESCRIPTION

IDCalc was developed to provide a simple way to view the expected isotope distribution for biological molecules measured by mass spectrometry.  The program also includes the the ability to consider enriched stable isotopes.

::DEVELOPER

MacCoss Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 IDCalc

:: MORE INFORMATION

Citation

Kubinyi, Analytica Chimica Acta, 247 (1991) 107-119.
The C, H, O, and N isotope abundances are specific to biological molecules
(Dwight E. Matthews personal communication)

Sadic / ProCoCoA 1.1b10 – Simple Atom Depth Index Calculator / Protein Core Composition Analyzer

Sadic / ProCoCoA 1.1b10

:: DESCRIPTION

Sadic/ProCoCoA is able to calculate the atom depth value for every atom of a protein structure, giving a lot of intrinsic information of 3D composition of the macromolecule and its core.

::DEVELOPER

SBL (Stuctural Biology Laboratory), University of Siena

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

Comput Biol Chem. 2013 Apr;43:29-34. doi: 10.1016/j.compbiolchem.2012.12.007. Epub 2012 Dec 31.
ProCoCoA: A quantitative approach for analyzing protein core composition.
Bottini S1, Bernini A, De Chiara M, Garlaschelli D, Spiga O, Dioguardi M, Vannuccini E, Tramontano A, Niccolai N.

MHScalculator 1.1 – Minimal Hitting Sets Calculator

MHScalculator 1.1

:: DESCRIPTION

MHScalculator is a free, command line tool for the computation of minimal hitting sets (MHSs) in hypergraphs.

::DEVELOPER

MHScalculator team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 MHScalculator

:: MORE INFORMATION

Citation:

C. Jungreuthmayer, G. Nair, S. Klamt, and J. Zanghellini.
Comparison and improvement of algorithms for computing minimal cut sets.
BMC Bioinformatics 14:318 (2013).

Renal Inner Medulla Free Energy Calculator

Renal Inner Medulla Free Energy Calculator

:: DESCRIPTION

The Renal Inner Medulla Free-Energy Calculator is a tool that allows the user to calculate steady-state mass balance and free-energy balance requirements for the renal inner medulla given a particular set of flows and concentrations in loops of Henle, collecting ducts, and vasa recta at the border between the inner and outer medulla of the mammalian kidney.

::DEVELOPER

Epithelial Systems Biology Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • JRE

:: DOWNLOAD

Renal Inner Medulla Free-Energy Calculator

:: MORE INFORMATION

GIC – Gene Importance Calculator

GIC

:: DESCRIPTION

GIC is a web server which can efficiently predict the essentiality of both protein-coding genes and long noncoding RNAs (lncRNAs) based on only sequence information.

::DEVELOPER

the Cui Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

GIC

:: MORE INFORMATION

Citation

Zeng P, Chen J, Meng Y, Zhou Y, Yang J, Cui Q.
Defining Essentiality Score of Protein-Coding Genes and Long Noncoding RNAs.
Front Genet. 2018 Oct 9;9:380. doi: 10.3389/fgene.2018.00380. PMID: 30356729; PMCID: PMC6189311.

stAIcalc – tAI Calculator based on Species-specific Weights

stAIcalc

:: DESCRIPTION

stAIcalc is a tAI(tRNA Adaptation Index) Calculator based on a species-specific inference of these weights.

::DEVELOPER

Tamir Tuller’s Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • MatLab

:: DOWNLOAD

stAIcalc

:: MORE INFORMATION

Citation

stAIcalc: tRNA adaptation index calculator based on species-specific weights.
Sabi R, Volvovitch Daniel R, Tuller T.
Bioinformatics. 2017 Feb 15;33(4):589-591. doi: 10.1093/bioinformatics/btw647.

Exit mobile version