M-Coffee: combining multiple sequence alignment methods with T-Coffee (Q25257876)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16556910%20AND%20SRC:MED&resulttype=core&format=json

18 January 2020

title

M-Coffee: combining multiple sequence alignment methods with T-Coffee (English)

1 reference

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18 January 2020

1 reference

0 references

1

1 reference

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18 January 2020

Desmond G. Higgins

series ordinal

3

1 reference

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18 January 2020

Cedric Notredame

series ordinal

4

1 reference

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18 January 2020

author name string

Orla O'Sullivan

series ordinal

2

1 reference

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18 January 2020

language of work or name

English

0 references

publication date

23 March 2006

1 reference

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18 January 2020

published in

Nucleic Acids Research

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18 January 2020

volume

34

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18 January 2020

issue

6

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18 January 2020

page(s)

1692-1699

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DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment

18 January 2020

cites work

1 reference

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ProbCons: Probabilistic consistency-based multiple sequence alignment

7 April 2017

1 reference

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MAFFT version 5: improvement in accuracy of multiple sequence alignment

7 April 2017

1 reference

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

7 April 2017

1 reference

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Multiple sequence alignment with the Clustal series of programs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

7 April 2017

1 reference

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SAGA: sequence alignment by genetic algorithm

7 April 2017

1 reference

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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

7 April 2017

1 reference

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

Multiple sequence alignments

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

Recent progress in multiple sequence alignment: a survey

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

HOMSTRAD: a database of protein structure alignments for homologous families

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

The alignment of sets of sequences and the construction of phyletic trees: an integrated method

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

Multiple sequence alignment using partial order graphs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

JPred: a consensus secondary structure prediction server

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

EVA: continuous automatic evaluation of protein structure prediction servers.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

COFFEE: an objective function for multiple sequence alignments

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

Weights for data related by a tree

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

JIGSAW: integration of multiple sources of evidence for gene prediction

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

Combining many multiple alignments in one improved alignment

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

Improved sensitivity of profile searches through the use of sequence weights and gap excision.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

Motif recognition and alignment for many sequences by comparison of dot-matrices.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

Consistency of optimal sequence alignments

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

Evaluation of iterative alignment algorithms for multiple alignment

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

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

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

PCMA: fast and accurate multiple sequence alignment based on profile consistency.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

Quality assessment of multiple alignment programs.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

An exact solution for the segment-to-segment multiple sequence alignment problem.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

DIALIGN: finding local similarities by multiple sequence alignment

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1410914

BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16556910

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKL091

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16556910%20AND%20SRC:MED&resulttype=core&format=json

18 January 2020

1 reference

2 references

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18 January 2020

PubMed publication ID

16556910

2 references