Tag: Effect

EFFECT 2013 – Automated Construction and Extraction of Features for Classification of Biological Sequences

EFFECT 2013

:: DESCRIPTION

EFFECT is an algorithmic framework for automated detection of functional signals in biological sequences.

::DEVELOPER

Computational Biology lab, George Mason University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • BioJava

:: DOWNLOAD

 EFFECT

:: MORE INFORMATION

Citation

Kamath U, De Jong K, Shehu A.
Effective automated feature construction and selection for classification of biological sequences.
PLoS One. 2014 Jul 17;9(7):e99982. doi: 10.1371/journal.pone.0099982. PMID: 25033270; PMCID: PMC4102475.

PROVEAN 1.1.5 – Protein Variation Effect Analyzer

PROVEAN 1.1.5

:: DESCRIPTION

PROVEAN is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.

::DEVELOPER

PROVEAN Team, J. Craig Venter Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PROVEAN

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Apr 6. pii: btv195.
PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels.
Choi Y, P Chan A

PLoS One. 2012;7(10):e46688. doi: 10.1371/journal.pone.0046688. Epub 2012 Oct 8.
Predicting the functional effect of amino acid substitutions and indels.
Choi Y, Sims GE, Murphy S, Miller JR, Chan AP.

BEclear 2.8.0 – Batch Effect Detection and Adjustment in DNA Methylation Data

BEclear 2.8.0

:: DESCRIPTION

BEclear enables researchers to identify those portions of the data that deviate statistically significant from the remaining data and to replace these portions by typical values reconstructed from neighboring data entries based on latent factor models.

::DEVELOPER

Chair of Computational Biology at the Saarland University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

BEclear

:: MORE INFORMATION

Citation

Akulenko R, Merl M, Helms V.
BEclear: Batch Effect Detection and Adjustment in DNA Methylation Data.
PLoS One. 2016 Aug 25;11(8):e0159921. doi: 10.1371/journal.pone.0159921. PMID: 27559732; PMCID: PMC4999208.

ENCoM – Exploring Protein Conformational Space and Effect of Mutations on Protein Function and Stability

ENCoM

:: DESCRIPTION

ENCoM is a coarse grained normal modes analysis method to evaluate thermostability of proteins.

::DEVELOPER

Najmanovich Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ENCoM

:: MORE INFORMATION

Citation

ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability.
Frappier V, Chartier M, Najmanovich RJ.
Nucleic Acids Res. 2015 Apr 16. pii: gkv343.

OEFinder 0.0.2 – Identify Ordering Effect Genes in Single Cell RNA-seq data

OEFinder 0.0.2

:: DESCRIPTION

OEFinder is a user interface to identify and visualize ordering effects in single-cell RNA-seq data.

::DEVELOPER

Ning Leng

:: SCREENSHOTS

OEFinder

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 OEFinder

:: MORE INFORMATION

Citation

OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data.
Leng N, Choi J, Chu LF, Thomson JA, Kendziorski C, Stewart R.
Bioinformatics. 2016 Jan 6. pii: btw004.

B-NEM – Boolean Nested Effect Models

B-NEM

:: DESCRIPTION

B-NEM combines the use of downstream effects with the higher resolution of signalling pathway structures in Boolean Networks.

::DEVELOPER

B-NEM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 B-NEM

:: MORE INFORMATION

Citation

Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models.
Pirkl M, Hand E, Kube D, Spang R.
Bioinformatics. 2015 Nov 17. pii: btv680.

mCSM – Predicting Effect of Mutations in Proteins using Graph-based Signatures

mCSM

:: DESCRIPTION

mCSM is a novel approach to the study of missense mutations which relies on graph-based signatures.

::DEVELOPER

Biosig Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

mCSM: predicting the effects of mutations in proteins using graph-based signatures.
Pires DE, Ascher DB, Blundell TL.
Bioinformatics. 2014 Feb 1;30(3):335-42. doi: 10.1093/bioinformatics/btt691.

snpEff 4.3T – Variant Annotation and Effect Prediction Tool

snpEff 4.3T

:: DESCRIPTION

snpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).

SnpSift is a collection of tools to manipulate VCF (variant call format) files.

SnpEffWrapper takes a VCF and applies Annotations from a GFF using SnpEff

::DEVELOPER

snpEff team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

snpEff / SnpEffWrapper

:: MORE INFORMATION

Citation

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM.
Fly (Austin). 2012 Apr-Jun;6(2):80-92.

Indelz 0.1 – Predict the Effects of Indels and non-sense Mutations

Indelz 0.1

:: DESCRIPTION

Indelz is bioinformatics method to predict the effects of indels and non-sense mutations Link to software.

::DEVELOPER

Alan Moses’ Computational Biology Lab ,University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Indelz

:: MORE INFORMATION

Citation

Ranking insertion, deletion and nonsense mutations based on their effect on genetic information
Amin Zia, Alan M Moses
BMC Bioinformatics. 2011; 12: 299.