Tag: FUGUE

FUGUE 0.2.3 – Haplotype Frequency Estimation

FUGUE 0.2.3

:: DESCRIPTION

FUGUE is the program used to construct haplotypes for the chromosome and linkage disequilibrium maps.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • MERLIN

:: DOWNLOAD

FUGUE

:: MORE INFORMATION

Citation:

Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S, Carter D, Papaspyridonos M, Livingstone S, Ganske R, Lohmussaar E, Zernant J, Tonisson N, Remm M, Magi R, Puurand T, Vilo J, Kurg A, Rice K, Deloukas P, Mott R, Metspalu A, Bentley DR, Cardon LR and Dunham I
A first-generation linkage disequilibrium map of human chromosome
Nature (2002) 418:544-548

Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Balding DJ, Donaldson MA, Studebaker JF, Ankener WM, Alfisi SV, Kuo FS, Camisa AL, Pazorov V, Scott KE, Carey BJ, Faith J, Katari G, Bhatti HA, Cyr JM, Derohannessian V, Elosua C, Forman AM, Grecco NM, Hock CR, Kuebler JM, Lathrop JA, Mockler MA, Nachtman EP, Restine SL, Varde SA, Hozza MJ, Gelfand CA, Broxholme J, Abecasis GR, Boyce-Jacino MT and Cardon LR
Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots.
Nat Genet (2003) 33:382-7

Prelude & Fugue – Predicting local Protein Structure, early Folding Regions and Structural Weaknesses

Prelude & Fugue

:: DESCRIPTION

Prelude & Fugue predict the local structure of a protein in terms of backbone dihedral angle domains, identify sequence regions that form early during folding, and locate structural weaknesses, defined as regions whose sequence is not optimal with respect to the tertiary fold.

::DEVELOPER

Service de Biomodélisation, Bioinformatique et Bioprocédés (3BIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Prelude and Fugue, predicting local protein structure, early folding regions and structural weaknesses.
Kwasigroch JM, Rooman M.
Bioinformatics. 2006 Jul 15;22(14):1800-2.

FUGUE 20160606 – Protein Structure Prediction using Remote Homology Detection

FUGUE 20160606

:: DESCRIPTION

FUGUE is a program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure. Given a query sequence (or a sequence alignment), FUGUE scans a database of structural profiles, calculates the sequence-structure compatibility scores and produces a list of potential homologues and alignments.

::DEVELOPER

the Mizuguchi Laboratory.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FUGUE

:: MORE INFORMATION

Citation

J. Shi, T. L. Blundell, and K. Mizuguchi (2001).
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure- dependent gap penalties.
J. Mol. Biol., 310, 243-257.