Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures (Q42619198)

3 November 2017

title

Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures (English)

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3 November 2017

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3 November 2017

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Cedric Notredame

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Jose Espinosa-Carrasco

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Jose Espinosa-Carrasco

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Cedrik Magis

Cedrik Magis

2

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Carsten Kemena

Carsten Kemena

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Giovanni Bussotti

Giovanni Bussotti

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Paolo Di Tommaso

Paolo Di Tommaso

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author name string

Jean-Francois Taly

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3 November 2017

Jia-Ming Chang

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3 November 2017

publication date

1 November 2011

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3 November 2017

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3 November 2017

volume

6

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3 November 2017

issue

11

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3 November 2017

page(s)

1669-1682

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Multiple sequence alignment.

3 November 2017

cites work

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https://api.crossref.org/works/10.1038/NPROT.2011.393

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

T-Coffee: A novel method for fast and accurate multiple sequence alignment

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Alignment uncertainty and genomic analysis

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

InterPro: the integrative protein signature database

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Rfam: updates to the RNA families database

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

The Pfam protein families database

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Amino acid substitution matrices from protein blocks

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Computational complexity of multiple sequence alignment with SP-score

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Clustal W and Clustal X version 2.0

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

MUSCLE: multiple sequence alignment with high accuracy and high throughput

31 March 2020

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https://api.crossref.org/works/10.1038/NPROT.2011.393

Recent developments in the MAFFT multiple sequence alignment program

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

ProbCons: Probabilistic consistency-based multiple sequence alignment

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

PROMALS3D: a tool for multiple protein sequence and structure alignments

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

COFFEE: an objective function for multiple sequence alignments

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

M-Coffee: combining multiple sequence alignment methods with T-Coffee

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

3DCoffee: combining protein sequences and structures within multiple sequence alignments

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

SSAP: sequential structure alignment program for protein structure comparison

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Protein homology detection by HMM-HMM comparison

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

R-Coffee: a method for multiple alignment of non-coding RNA

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark

31 March 2020

1 reference

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T-RMSD: a fine-grained, structure-based classification method and its application to the functional characterization of TNF receptors

31 March 2020

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PhyloWidget: web-based visualizations for the tree of life

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Rfold: an exact algorithm for computing local base pairing probabilities

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

RNAalifold: improved consensus structure prediction for RNA alignments

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Analysis and classification of RNA tertiary structures

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Transcription factor map alignment of promoter regions

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

The RCSB Protein Data Bank: redesigned web site and web services

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

BLAST : architecture and applications

31 March 2020

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.393

Optimal alignments in linear space

31 March 2020

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21979275

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NPROT.2011.393

1 reference

3 November 2017

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