TSEMA specifications

Information


Unique identifier OMICS_11014
Name TSEMA
Interface Web user interface
Restrictions to use None
Input data The initial input for the system are the two families of homologous proteins for which the user wants to predict the mapping. There is a set of advanced options to control the Monte Carlo algorithm which are intentionally blurred unless the user decides to enable them. For the two families of proteins, the user can either submit two phylogenetic trees (in Newick format) or two multiple sequence alignments in a format compatible with ClustalW. In the second case, the system generates the phylogenetic trees from the alignments using the neighbour joining algorithm implemented in ClustalW.
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Publication for TSEMA

TSEMA in publications

 (3)
PMCID: 3852051
PMID: 24564758
DOI: 10.1186/1471-2105-14-S15-S18

[…] proteins (paralogs), however, the mapping task becomes difficult., there are only a handful of existing approaches for the paralog mapping problem [-]. izarzugaza et al. [], in their method tag-tsema, and most earlier approaches establish mappings by swapping rows and columns of the distance matrices to achieve similarity between the matrices. tillier et al. [] take a different approach […]

PMCID: 2263026
PMID: 18215279
DOI: 10.1186/1471-2105-9-35

[…] families show similar phylogenetic trees. even if this is true for most cases, it has been shown that the trees of some particular interacting families are not correlated [,]. in these cases, tag_tsema, or any other method based on tree-correlations, would not be expected to work. to quantify this, we studied the relationship between accuracy and tree similarity for both the real mapping […]


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TSEMA institution(s)
National Center for Biotechnology (CNB-CSIC) C/Darwin, Cantoblanco, Madrid, Spain; National Bioinformatics Institute (INB), Barcelona Supercomputer Centre C/Jordi Girona, Barcelona, Spain; Department of Biochemistry and Molecular Biology, Biomolecular Structure and Modelling Unit, University College London, London, UK

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