PSI/TM-Coffee statistics

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Citations per year

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Popular tool citations

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Tool usage distribution map

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Associated diseases

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PSI/TM-Coffee specifications

Information


Unique identifier OMICS_11524
Name PSI/TM-Coffee
Interface Web user interface
Restrictions to use None
Input data Protein sequences
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Cedric Notredame <>

Information


Unique identifier OMICS_11524
Name PSI/TM-Coffee
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Protein sequences
Input format FASTA
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Source code URL http://www.tcoffee.org/Projects/tcoffee/index.html#DOWNLOAD
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Cedric Notredame <>

Publications for PSI/TM-Coffee

PSI/TM-Coffee in pipeline

2017
PMCID: 5449183
PMID: 28504641
DOI: 10.7554/eLife.24303.028

[…] a representative sequence was kept and other sequences were discarded. this procedure resulted in 116 sequences. multiple sequence alignments of ktra and ktrb homologs were then generated using psi/tm-coffee (). the initial multiple sequence alignments were accordingly refined by (i) considering the pairwise alignments between ktra/b sequences from v. alginolyticus and b. subtilis, […]


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PSI/TM-Coffee in publications

 (3)
PMCID: 5662749
PMID: 29084970
DOI: 10.1038/s41598-017-14438-1

[…] information for all plasmids (supplementary table ) and primers (supplementary table ) used in this study., multiple sequence alignment of mal11 with other transporters was performed using psi/tm-coffee. jalview was used for alignment visualization and pairwise alignment calculations. transporter sequences were found with the following uniprot accession numbers: mal11 (p54038), xyle […]

PMCID: 5449183
PMID: 28504641
DOI: 10.7554/eLife.24303.028

[…] a representative sequence was kept and other sequences were discarded. this procedure resulted in 116 sequences. multiple sequence alignments of ktra and ktrb homologs were then generated using psi/tm-coffee (). the initial multiple sequence alignments were accordingly refined by (i) considering the pairwise alignments between ktra/b sequences from v. alginolyticus and b. subtilis, […]

PMCID: 5122774
PMID: 27758859
DOI: 10.1074/jbc.M116.743062

[…] against a. thaliana and yeast gpcat were carried out to verify homology. the selected sequences were also analyzed by blink (ncbi) to exclude contaminants. alignments were made using the t-coffee psi/tm-coffee () web service, unless otherwise indicated in the figure legends. alignments were subjected to maximum likelihood analysis in mega version 6.0.6 (), using an 85% limit for partial gaps. […]


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PSI/TM-Coffee institution(s)
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Department of Computer Science, National Chengchi University, Taipei, Taiwan
PSI/TM-Coffee funding source(s)
Plan Nacional [BFU2011-28575]; Center for Genomic Regulation (CRG); ‘Fundació Obra Social la Caixa’; Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017’ [SEV-2012–0208]; Center for Genomic Regulation (CRG)

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