PPalign: optimal alignment of Potts models representing proteins with direct coupling information

PPalign: optimal alignment of Potts models representing proteins with direct coupling information

Background: To assign structural and functional annotations to the ever increasing amount of sequenced proteins, the main approach relies on sequence-based homology search methods, e.g. BLAST or the current state-of-the-art methods based on profile Hidden Markov Models, which rely on significant ali...

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Bibliographic Details
Main Authors: Coste, F. (Author), Talibart, H. (Author)
Format: Article
Language:English
Published: BioMed Central Ltd 2021
Subjects:
algorithm
Algorithms
Alignment
amino acid sequence
Amino Acid Sequence
article
coevolution
Coevolution
Computational bottlenecks
Couplings
Direct coupling analysis
Functional annotation
genetics
Hidden Markov models
Homology
human
Humans
Integer linear programming
Integer linear programming formulation
Integer programming
Optimal alignments
Pairwise alignment
Pairwise sequence alignment
Potts model
prediction
Profile hidden Markov model
protein
Proteins
sequence alignment
Sequence alignment
Sequence Alignment
sequence homology
Sequence Homology
State-of-the-art methods
system analysis
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