APOLLO – Assess Protein Single or Multiple Model(s)

APOLLO

:: DESCRIPTION

APOLLO pairwise is a program to assess the quality of a pool of structure models predicted for a protein. Teh software evaluates the absolute and/or relative qualities of multiple models or a single model

::DEVELOPER

Dr. Jianlin Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 APOLLO

:: MORE INFORMATION

Citation

Zheng Wang, Jesse Eickholt, and Jianlin Cheng, (2011)
APOLLO: A Quality Assessment Service for Single and Multiple Protein Models,
Bioinformatics, 27(12), 1715-1716.

vntrTest 0.52 – Assess Association of VNTR Fragment Length Genotypes

vntrTest 0.52

:: DESCRIPTION

vntrTest is a program for assessing association of VNTR fragment length genotypes with either continuous or case-control outcomes.

::DEVELOPER

Dr Lachlan J Coin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 vntrTest

:: MORE INFORMATION

Citation

Hum Mol Genet. 2012 Aug 15;21(16):3727-38. doi: 10.1093/hmg/dds187.
Novel association approach for variable number tandem repeats (VNTRs) identifies DOCK5 as a susceptibility gene for severe obesity.
El-Sayed Moustafa JS, Eleftherohorinou H, de Smith AJ, Andersson-Assarsson JC, Alves AC, Hadjigeorgiou E, Walters RG, Asher JE, Bottolo L, Buxton JL, Sladek R, Meyre D, Dina C, Visvikis-Siest S, Jacobson P, Sj?str?m L, Carlsson LM, Walley A, Falchi M, Froguel P, Blakemore AI, Coin LJ.

Conserve IV 1.4b – Assess & Prioritorize Conservation Schemes based on Phylogenies

Conserve IV 1.4b

:: DESCRIPTION

Conserve IV is an application for calculating diversity in site-based conservation and assessing preservation schemes. Specifically, it calculates diversity metrics over a phylogeny or series of phylogenies. Individual taxa can be included or excluded from calculations, simulating the state of their preservation and possible accompanying loss of evolutionary history. Taxa can be grouped into sets manually or via several automatic methods, and these sets activated or inactivated as one. Where multiple phylogenies are provided, confidence limits are calculated for diversity metrics. Finally, capability is provided for summing external costs, expenditure that is specific to preserving individual taxa.

::DEVELOPER

Paul-Michael Agapow and Austin Burt (a.burt@imperial.ac.uk), Dept. Biology, University College London

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

 Conserve IV

:: MORE INFORMATION

Overall LD – Assess the Overall Linkage Disequilibrium

Overall LD

:: DESCRIPTION

Overall LD is a program to assess the overall Linkage Disequilibrium (LD) over several markers and assess the LD between groups of markers.

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Overall LD

:: MORE INFORMATION

Citation

Ann Hum Genet. 1999 Mar;63(Pt 2):167-79.
Assessing linkage disequilibrium in a complex genetic system. I. Overall deviation from random association.
Zhao H, Pakstis AJ, Kidd JR, Kidd KK.

ANOLEA 2.4.2-2 – Assess the Quality of a 3D Protein Structure

ANOLEA 2.4.2-2

:: DESCRIPTION

ANOLEA (Atomic Non-Local Environment Assessment) is a server to assess the quality of a three – dimensional protein structure. It uses a statistical potential at the atomic level and gives an energy profile as ouput. Also, the user can choose to have a molecular graphical output representation of the energy profile.

::DEVELOPER

Francisco Melo Ledermann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ANOLEA

:: MORE INFORMATION

Citation

Proc Int Conf Intell Syst Mol Biol. 1997;5:187-90.
ANOLEA: a www server to assess protein structures.
Melo F, Devos D, Depiereux E, Feytmans E.

MUDE 1.0 – Assess MS/MS Spectra Assignments

MUDE 1.0

:: DESCRIPTION

mude (multivariate decoy database analysis) is a set of programs implementing the framework to assess MS/MS spectra assignments

:: DEVELOPER

By Cerqueira, Fabio (fabio.cerqueira@ufv.br); Graber, Armin; Schwikowski, Benno; Baumgartner, Christian.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • JAVA

:: DOWNLOAD

 MUDE

:: MORE INFORMATION

Citation

MUDE: a new approach for optimizing sensitivity in the target-decoy search strategy for large-scale peptide/protein identification.
Cerqueira FR, Graber A, Schwikowski B, Baumgartner C.
J Proteome Res. 2010 May 7;9(5):2265-77. doi: 10.1021/pr901023v.

TOROCOR 1.0 – Assess the Association between Spatially Autocorrelated Variables using Torus-translation tests

TOROCOR 1.0

:: DESCRIPTION

TOROCOR is designed (1) to characterise the spatial autocorrelation of quantitative and/or qualitative variables and (2) to test the significance of the association between variables, notably using torus-translation randomisations. The latter procedure removes the bias of classical tests applied on spatially autocorrelated variables where samples cannot be considered as independent (classical tests tend to be liberal, i.e. rejecting too often the null hypothesis that there is no association between variables).

::DEVELOPER

Olivier Hardy @ Evolutionary Biology & Ecology, Université Libre de Bruxelles

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 TOROCOR

:: MORE INFORMATION

Consel 0.20 – Assess Confidence of Phylogenetic Tree Selection

Consel 0.20

:: DESCRIPTION

CONSEL is a program package consists of small programs written in C language. It calculates the probability value (i.e., p-value) to assess the confidence in the selection problem. Although CONSEL is applicable to any selection problem, it is mainly designed for the phylogenetic tree selection. CONSEL does not estimate the phylogenetic tree by itself, but CONSEL does read the output of the other phylogenetic packages, such as Molphy, PAML, PAUP*, TREE-PUZZLE, and PhyML. CONSEL calculates the p-value using several testing procedures; the bootstrap probability, the Kishino-Hasegawa test, the Shimodaira-Hasegawa test, and the weighted Shimodaira-Hasegawa test. In addition to these conventional tests, CONSEL calculates the p-value based on the approximately unbiased test using the multi-scale bootstrap technique.

::DEVELOPER

Hidetoshi Shimodaira

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows

:: DOWNLOAD

 CONSEL

:: MORE INFORMATION

Citation:

Shimodaira, H. & Hasegawa, M.
CONSEL: for assessing the confidence of phylogenetic tree selection.
Bioinformatics 17, 1246-1247 (2001).

Epistasis-HS – Assess the Degree of Epistasis for a given Trait

Epistasis-HS

:: DESCRIPTION

Epistasis-HS allow you to assess the degree of epistasis for a given trait between a pair of maternal or paternal half-sib families. You are only able to use this program to calculate epistasis between a pair of half-sib families.  If your mating structure involves multiple half-sib families (i.e., k > 2) you will need to recalculate estimates among all the possible pairwise half-sib groupings  (i.e., k*(k-1) / 2 pairwise combinations).

::DEVELOPER

Roy G. Danzmann

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Epistasis-HS

:: MORE INFORMATION

CPC 0.9r2 – Assess Protein-coding Potential of Transcripts

CPC 0.9r2

:: DESCRIPTION

CPC (Coding Potential Calculator) is a software to assess the protein-coding potential of a transcript (i.e whether a cDNA/RNA transcript could encode a peptide or not) based on six biologically meaningful sequence features. Tenfold cross-validation on the training dataset and further testing on several large datasets showed that CPC can discriminate coding from noncoding transcripts with high accuracy. Furthermore, CPC also runs an order-of-magnitude faster than a previous state-of-the-art tool and has higher accuracy.

::DEVELOPER

Center for Bioinformatics, Peking University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CPC

:: MORE INFORMATION

Citation:

Kong, L., Y. Zhang, Z.Q. Ye, X.Q. Liu, S.Q. Zhao, L. Wei, and G. Gao. 2007.
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.
Nucleic Acids Res 36: W345-349.