Tag: Multiple Alignment

Gblocks 0.91b – Selection of Conserved Blocks from multiple alignments for their use in Phylogenetic Snalysis

Gblocks 0.91b

:: DESCRIPTION

Gblocks is a computer program written in C that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis.

::DEVELOPER

Castresana Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX

:: DOWNLOAD

  Gblocks

:: MORE INFORMATION

Citation:

Talavera, G., and Castresana, J. (2007).
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.
Systematic Biology 56, 564-577.

Facet v1.4 – Multiple Alignment Accuracy Estimation and Parameter Advising

Facet v1.4

:: DESCRIPTION

Facet (Feature-based accuracy estimator) computes a single estimate of accuracy as a linear combination of efficiently-computable feature functions.

::DEVELOPER

Dr. Dan DeBlasio

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

Facet

:: MORE INFORMATION

Citation

J Comput Biol. 2013 Apr;20(4):259-79. doi: 10.1089/cmb.2013.0007. Epub 2013 Mar 14.
Accuracy estimation and parameter advising for protein multiple sequence alignment.
Kececioglu J, DeBlasio D.

Magma 1.0 – Multiple Aligner of Genomic Multiple Alignments

Magma 1.0

:: DESCRIPTION

Magma is a fast, sensitive tool for whole regulome motif-finding in eukaryotic genomes

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • Perl

:: DOWNLOAD

 Magma

:: MORE INFORMATION

Citation

J Comput Biol. 2012 Feb;19(2):139-47. doi: 10.1089/cmb.2011.0249.
Fast, sensitive discovery of conserved genome-wide motifs.
Ihuegbu NE, Stormo GD, Buhler J.

BetaTPred2: Prediction of Beta-turns in Proteins using Neural Networks and Multiple Alignment

BetaTPred2

:: DESCRIPTION

The aim of BetaTPred2 server is to predict Beta turns in proteins from multiple alignment by using neural network from the given amino acid sequence. For ? turn prediction, it uses the position specific score matrices generated by PSI-BLAST and secondary structure predicted by PSIPRED. The net is trained and tested on a set of 426 non-homologous protein chains with 7-fold cross-validation. It predicts ? turns in proteins with residue accuracy of 75.5% and MCC value of 0.43.

::DEVELOPER

BetaTPred2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Kaur, H. and Raghava, G.P.S.
Prediction of beta-turns in proteins from multiple alignment using neural network.
Protein Science 2003 12: 627-634

AlphaPred – Prediction of Alpha-turns in Proteins using Multiple Alignment and Secondary Structure Information

AlphaPred

:: DESCRIPTION

The AlphaPred server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.

::DEVELOPER

Dr. G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Kaur H & Raghava GP. (2004).
Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information.
Proteins. 55: 83-90

GammaPred – Prediction of Gamma-turns in Proteins using Multiple Alignment and Secondary Structure Information

GammaPred

:: DESCRIPTION

The GammaPred server predicts the gamma turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure. Two neural networks with a single hidden layer have been used where the first sequence-to-structure network is trained on PSI-BLAST obtained position specific matrices. The filtering has been done by second structure-to-structure network trained on output of first net and PSIPRED predicted secondary structure. The training has been carried out using error backpropagation with a sum of square error function(SSE).

::DEVELOPER

Dr. G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Kaur, H. and Raghava, G.P.S. (2003)
A neural network based method for prediction of gamma-turns in proteins from multiple sequence alignment.
Protein Science 12: 923-929.

PSAweb – Analysis of Protein Sequence and Multiple Alignment

PSAweb

:: DESCRIPTION

PSAweb is a web server, developed to analyze the amino acid sequence and multiple sequence alignment of proteins. This is a comprehensive on-line Internet tool that allows the rapid visualization of an analysis, by output in GIF format. It assists the user in analyzing and presenting the primary structure of proteins and mutiple alignment of protein sequences

::DEVELOPER

Dr. G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Raghava, G. P. S. (2001)
A graphical web server for the analysis of protein sequences and alignment.
Biotech Software and Internet Report 2: 255-8.

MONKEY 2.0 – Identify Matches to DNA Motifs in Multiple Alignments

MONKEY 2.0

:: DESCRIPTION

MONKEY is a set of programs designed to search alignments of non-coding DNA sequence for matches to matrices representing the sequence specificity of transcription factors.MONKEY employs probabilistic models of factor specificity and binding-site evolution, on which basis we compute the likelihood that putative sites are conserved and assign statistical significance to each hit.

::DEVELOPER

Alan Moses’ Computational Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MONKEY

:: MORE INFORMATION

Citation

Moses et. al.
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
Genome Biol. 2004;5(12):R98

jpHMM 201503 – Compare a Sequence to a Multiple Alignment of a Sequence Family

jpHMM 201503

:: DESCRIPTION

jpHMM (jumping profile Hidden Markov Model) is a probabilistic approach to compare a sequence to a multiple alignment of a sequence family. The jpHMM web server at GOBICS is a tool for the detection of genomic recombinations in HIV-1 and HBV.

jpHMM Online Version

::DEVELOPER

the Department of Bioinformatics of the University of Göttingen and the Los Alamos HIV Sequence Database Group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

jpHMM

:: MORE INFORMATION

Citation

A.-K. Schultz, M. Zhang, T. Leitner, C. Kuiken, B. Korber, B. Morgenstern, M. Stanke.
A Jumping Profile Hidden Markov Model and Applications to Recombination Sites in HIV and HCV Genomes.
BMC Bioinformatics 7:265. 2006

PETfold 2.0 / PETcofold 3.2 – Folding of Multiple Alignment of RNA sequences

PETfold 2.0 / PETcofold 3.2

:: DESCRIPTION

PETfold: Phylogenetic, Evolutionary and Thermodynamic folding of a multiple alignment of RNA sequences.

PETcofold: Integrated framework with PETfold to fold and search for RNA-RNA interactions between two multiple alignments of RNA sequences.

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PETfold , PETcofold

:: MORE INFORMATION

Citation:

Seemann SE, Menzel P, Backofen R, Gorodkin J
“The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences.”,
Nucleic Acid Res., 39(Web Server issue):W107-11, 2011.

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