Multiple Sequence Alignment
18 papers with code • 3 benchmarks • 0 datasets
Benchmarks
These leaderboards are used to track progress in Multiple Sequence Alignment
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Latest papers with no code
Aligning 415 519 proteins in less than two hours on PC
Importantly, its implementation is highly optimised and parallelised to make the most of modern computer platforms.
Identifying relevant positions in proteins by Critical Variable Selection
This suggests that Critical Variable Selection is able to identify in a Multiple Sequence Alignment a core of sites encoding functional and structural information.
Statistically-Consistent k-mer Methods for Phylogenetic Tree Reconstruction
Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment.
Predicting diverse M-best protein contact maps
Existing EC analysis methods predict only a single contact map for a given protein, which may have low accuracy especially when the protein under prediction does not have a large number of sequence homologs.
Multiple sequence alignment for short sequences
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists.
Liquid-theory analogy of direct-coupling analysis of multiple-sequence alignment and its implications for protein structure prediction
The direct-coupling analysis is a powerful method for protein contact prediction, and enables us to extract "direct" correlations between distant sites that are latent in "indirect" correlations observed in a protein multiple-sequence alignment.
A Novel Method for Comparative Analysis of DNA Sequences by Ramanujan-Fourier Transform
To address the different lengths in Euclidean space of RFT coefficients, we pad zeros to short DNA binary sequences so that the binary sequences equal the longest length in the comparison sequence data.
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection.
Efficient Inference in Phylogenetic InDel Trees
Accurate and efficient inference in evolutionary trees is a central problem in computational biology.
