Multiple Sequence Alignment

16 papers with code • 3 benchmarks • 0 datasets

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Most implemented papers

Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations

idrori/cu-tsp 9 Nov 2019

Our dataset consists of amino acid sequences, Q8 secondary structures, position specific scoring matrices, multiple sequence alignment co-evolutionary features, backbone atom distance matrices, torsion angles, and 3D coordinates.

Phylogenetic automata, pruning, and multiple alignment

ihh/transducer-tutorial 22 Mar 2011

We present an extension of Felsenstein's algorithm to indel models defined on entire sequences, without the need to condition on one multiple alignment.

Ultra-large alignments using Phylogeny-aware Profiles

smirarab/sepp 5 Apr 2015

Many biological questions, including the estimation of deep evolutionary histories and the detection of remote homology between protein sequences, rely upon multiple sequence alignments (MSAs) and phylogenetic trees of large datasets.

QuickProbs 2: towards rapid construction of high-quality alignments of large protein families

refresh-bio/QuickProbs 30 Aug 2016

Increasing size of sequence databases caused by the development of high throughput sequencing, poses multiple alignment algorithms to face one of the greatest challenges yet.

Optimizing scoring function of dynamic programming of pairwise profile alignment using derivative free neural network

yamada-kd/nepal 30 Aug 2017

Nepal, the pairwise profile aligner with the novel scoring function significantly improved both alignment sensitivity and precision, compared to aligners with the existing functions.

Align-RUDDER: Learning From Few Demonstrations by Reward Redistribution

ml-jku/align-rudder 29 Sep 2020

For such complex tasks, the recently proposed RUDDER uses reward redistribution to leverage steps in the Q-function that are associated with accomplishing sub-tasks.

DLPAlign: A Deep Learning based Progressive Alignment Method for Multiple Protein Sequences

kuangmeng/DLPAlign 21 Nov 2020

This paper proposed a novel and straightforward approach to improve the accuracy of progressive multiple protein sequence alignment method.

MSA Transformer

The-AI-Summer/self-attention-cv 13 Feb 2021

Unsupervised protein language models trained across millions of diverse sequences learn structure and function of proteins.

Algorithms and Complexity on Indexing Founder Graphs

algbio/founderblockgraphs 25 Feb 2021

We study the problem of matching a string in a labeled graph.

MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences

haschka/mnhn-tree-tools Bioinformatics 2021

We introduce MNHN-Tree-Tools, a high performance set of algorithms that builds multi-scale, nested clusters of sequences found in a FASTA file.