PASTA 2.0 – Protein Aggregation Prediction

PASTA 2.0

:: DESCRIPTION

PASTA (Prediction of amyloid structure aggregation) is a web server for the analysis of amino acid sequences. It predicts which portions of a given input sequence are more likely to stabilize the cross-beta core of fibrillar aggregates.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PASTA

:: MORE INFORMATION

Citation:

PASTA 2.0: an improved server for protein aggregation prediction.
Walsh I, Seno F, Tosatto SC, Trovato A.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W301-7. doi: 10.1093/nar/gku399.

Antonio Trovato, Flavio Seno and Silvio C.E. Tosatto.
The PASTA server for protein aggregation prediction
Protein Engineering Design & Selection, 20(10):521-523. (2007)

AGGRESCAN – Prediction and Evaluation of “hot spots” of Aggregation in Polypeptides

AGGRESCAN

:: DESCRIPTION

AGGRESCAN is a web-based software for the prediction of aggregation-prone segments in protein sequences, the analysis of the effect of mutations on protein aggregation propensities and the comparison of the aggregation properties of different proteins or protein sets.

::DEVELOPER

Xavier Daura

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2007 Feb 27;8:65.
AGGRESCAN: a server for the prediction and evaluation of “hot spots” of aggregation in polypeptides.
Conchillo-Solé O1, de Groot NS, Avilés FX, Vendrell J, Daura X, Ventura S.

HyDRA – Hybrid Distance-Score Rank Aggregation software for Gene Prioritization

HyDRA

:: DESCRIPTION

HyDRA is a new approach to genomic data aggregation which combines the advantages of score-based and combinatorial aggregation techniques.

::DEVELOPER

Olgica Milenkovic’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
MatLab

:: DOWNLOAD

HyDRA

:: MORE INFORMATION

Citation

HyDRA: Gene Prioritization via Hybrid Distance-Score Rank Aggregation.
Kim M, Farnoud F, Milenkovic O.
Bioinformatics. 2014 Nov 18. pii: btu766.

DAS tool 1.1.3 – Recovery of Genomes from Metagenomes via Dereplication, Aggregation, and Scoring Strategy

DAS tool 1.1.3

:: DESCRIPTION

DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.

::DEVELOPER

Banfield Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

DAS Tool

:: MORE INFORMATION

Citation

Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, Banfield JF.
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy.
Nat Microbiol. 2018 Jul;3(7):836-843. doi: 10.1038/s41564-018-0171-1. Epub 2018 May 28. PMID: 29807988; PMCID: PMC6786971.

MuCor – Mutation Aggregation and Correlation

MuCor

:: DESCRIPTION

MuCor is software to aggregate variant information sourced from multiple VCF files (and some others, see below) into a variety of summary files with varying levels of detail and statistics.

::DEVELOPER

blachly lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX
Python

:: DOWNLOAD

MuCor

:: MORE INFORMATION

Citation:

MuCor: Mutation Aggregation and Correlation.
Kroll KW, Eisfeld AK, Lozanski G, Bloomfield CD, Byrd JC, Blachly JS.
Bioinformatics. 2016 Jan 23. pii: btw028

FamAgg 1.21.2 – Pedigree Analysis and Familial Aggregation

FamAgg 1.21.2

:: DESCRIPTION

FamAgg is an open source R package that contains both established and novel methods to investigate familial aggregation of traits in large pedigrees.

::DEVELOPER

Eurac Biomedical Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
R / BioConductor

:: DOWNLOAD

FamAgg

:: MORE INFORMATION

Citation

FamAgg: an R Package to Evaluate Familial Aggregation of Traits in Large Pedigrees.
Rainer J, Taliun D, D’Elia Y, Pattaro C, Domingues FS, Weichenberger CX.
Bioinformatics. 2016 Jan 22. pii: btw019.

ACT – Aggregation and Correlation Toolbox for analyses of Genome Tracks

ACT

:: DESCRIPTION

The ACT (aggregation and correlation toolbox) is an aggregation and correlation toolbox for analyses of genome tracks.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

ACT

:: MORE INFORMATION

Citation

J Jee*, J Rozowsky*, KY Yip*, L Lochovsky, R Bjornson, G Zhong, Z Zhang, Y Fu, J Wang, Z Weng, M Gerstein.
ACT: Aggregation and Correlation Toolbox for Analyses of Genome Tracks. (2011)
Bioinformatics. 2011 Apr 15;27(8):1152-4.