Tag: Structure

EIGENSOFT 7.2.1 – Population Structure , Eigenanalysis & Stratification

EIGENSOFT 7.2.1

:: DESCRIPTION

EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.

::DEVELOPER

Reich laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 EIGENSOFT

:: MORE INFORMATION

Citation:

Nature Genetics 38, 904 – 909 (2006) Published online: 23 July 2006; | doi:10.1038/ng1847
Principal components analysis corrects for stratification in genome-wide association studies
Alkes L Price, Nick J Patterson, Robert M Plenge, Michael E Weinblatt, Nancy A Shadick & David Reich

Population Structure and Eigenanalysis
Nick Patterson, Alkes L. Price, David Reich
December 2006 Issue of PLoS Genetics

NASSAM – 3D Pattern Searching in Nucleic Acid Structures

NASSAM

:: DESCRIPTION

The NASSAM (Nucleic Acid Search for Substructures And Motifs) program searches for 3D motifs and patterns of bases in RNA (and RNA associated) PDB formatted query structures.

::DEVELOPER

The Molecular Function Regulation Lab (M. Firdaus Raih research group)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Hazrina Y. Hamdani, Sri D. Appasamy, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. 2012.
NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules.
Nucleic Acids Research. doi: 10.1093/nar/gks513.

ProtDCal 4.5 – Computing Multiple Numerical Descriptors for Protein Sequences and Structures

ProtDCal 4.5

:: DESCRIPTION

ProtDCal (Protein Descriptors Calculation program) is a new computational software suite capable of generating tens of thousands of features considering both sequence-based and 3D-structural descriptors.

::DEVELOPER

ProtDCal team

:: SCREENSHOTS

ProtDCal

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 ProtDCal

:: MORE INFORMATION

Citation

ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins.
Ruiz-Blanco YB, Paz W, Green J, Marrero-Ponce Y.
BMC Bioinformatics. 2015 May 16;16:162. doi: 10.1186/s12859-015-0586-0.

MotiveValidator 1.1.15.8.8e – Validate Ligand and Residue Structure in Biomolecular Complexes

MotiveValidator 1.1.15.8.8e

:: DESCRIPTION

MotiveValidator is a platform for a set of applications designed to help you determine whether a residue or a ligand in a biomolecule or biomolecular complex is structurally complete and correctly annotated according to its models stored in the wwPDB Chemical Component Dictionary (wwPDB CCD).

::DEVELOPER

MotiveValidator team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

MotiveValidator

:: MORE INFORMATION

Citation

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes.
Vařeková RS, Jaiswal D, Sehnal D, Ionescu CM, Geidl S, Pravda L, Horský V, Wimmerová M, Koča J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W227-33. doi: 10.1093/nar/gku426.

LOCPRED – Local Backbone Structure Prediction of Proteins

LOCPRED

:: DESCRIPTION

LOCPRED is a tool for local structure prediction from protein sequence using a structural alphabet approach.

::DEVELOPER

the DSIMB bioinformatic group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

In Silico Biol. 2004;4(3):381-6.
Local backbone structure prediction of proteins.
de Brevern AG1, Benros C, Gautier R, Valadié H, Hazout S, Etchebest C.

PredyFlexy – Flexibility and Local Structure prediction from sequence

PredyFlexy

:: DESCRIPTION

PredyFlexy is designed to predict local protein structures and protein flexibility from its sequence. Results can be visualised at the amino acid level through a table and graphics.

::DEVELOPER

the DSIMB bioinformatic group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PredyFlexy

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W317-22. doi: 10.1093/nar/gks482. Epub 2012 Jun 11.
PredyFlexy: flexibility and local structure prediction from sequence.
de Brevern AG1, Bornot A, Craveur P, Etchebest C, Gelly JC.

STRAT 1.1 – Companion program to Structure

STRAT 1.1

:: DESCRIPTION

STRAT is a companion program to structure. This is a structured association method, for use in association mapping, enabling valid case-control studies even in the presence of population structure.

::DEVELOPER

Pritchard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 STRAT

:: MORE INFORMATION

Citation:

J.K. Pritchard, M. Stephens, N.A. Rosenberg and P. Donnelly, 2000.
Association mapping in structured populations.
Am J. Hum Genet. 67:170-181

Structure 2.3.4 – Use Multi-locus Genotype Data to Investigate Population Structure

Structure 2.3.4

:: DESCRIPTION

Structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.

::DEVELOPER

Pritchard Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 Structure

:: MORE INFORMATION

Citation:

Daniel Falush, Matthew Stephens, and Jonathan K. Pritchard
Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies
Genetics, Vol. 164, 1567-1587,

Kolmogorov – Compression-based Classification of Biological Sequences and Structures

Kolmogorov

:: DESCRIPTION

Kolmogorov is a multistep approach to classify and cluster Biological Sequences and Structures, via Compression.

::DEVELOPER

Raffaele Giancarlo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX / Windows
  • Perl
  • BioPerl

:: DOWNLOAD

 Kolmogorov

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Jul 13;8:252.
Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.
Ferragina P1, Giancarlo R, Greco V, Manzini G, Valiente G.

TITINdb – Database of Titin Structure, Sequence, Isoform, Variant and Disease Information

TITINdb

:: DESCRIPTION

TITINdb is a web application which integrates titin structure, sequence, isoform, variant and disease information.

::DEVELOPER

Fraternali lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Laddach A, Gautel M, Fraternali F.
TITINdb-a computational tool to assess titin’s role as a disease gene.
Bioinformatics. 2017 Nov 1;33(21):3482-3485. doi: 10.1093/bioinformatics/btx424. PMID: 29077808; PMCID: PMC5860166.