Search Results - "Alignment"

LCSkPOA: enabling banded semi-global partial order alignments via efficient and accurate backbone generation through extended LCSk+.

Authors: Weerakoon M Saunders CT Heaton H

Source: BMC bioinformatics [BMC Bioinformatics] 2025 Nov 25; Vol. 26 (1), pp. 284. Date of Electronic Publication: 2025 Nov 25.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: Algorithms* , Sequence Alignment*/methods , Software*

Coevolutionary signals in multiple sequence alignments improve virulence factor prediction with an MSA Transformer.

Authors: Kim T Cho C Lee D et al.

Source: Scientific reports [Sci Rep] 2025 Nov 19; Vol. 15 (1), pp. 40688. Date of Electronic Publication: 2025 Nov 19.

Publication Type: Journal Article

Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

MeSH Terms: Virulence Factors*/genetics , Virulence Factors*/chemistry , Sequence Alignment*/methods , Evolution, Molecular* , Computational Biology*/methods , Bacterial Proteins*/genetics , Bacterial Proteins*/chemistry, Algorithms ; Amino Acid Sequence ; Deep Learning ; Sequence Analysis, Protein/methods

Evaluating the significance of embedding-based protein sequence alignment with clustering and double dynamic programming for remote homology.

Authors: Spicer R Raychawdhary N Danwada S et al.

Source: Scientific reports [Sci Rep] 2025 Nov 12; Vol. 15 (1), pp. 39601. Date of Electronic Publication: 2025 Nov 12.

Publication Type: Journal Article

Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Proteins*/genetics , Sequence Alignment*/methods , Sequence Homology, Amino Acid* , Sequence Analysis, Protein*/methods, Cluster Analysis ; Algorithms ; Computational Biology/methods ; Amino Acid Sequence ; Dynamic Programming

Enzyme sequence optimisation via Gromov-Wasserstein Autoencoders integrating MSA techniques.

Authors: Wang X Li Y Hou X et al.

Source: Journal of enzyme inhibition and medicinal chemistry [J Enzyme Inhib Med Chem] 2025 Dec; Vol. 40 (1), pp. 2524742. Date of Electronic Publication: 2025 Jul 03.

Publication Type: Journal Article

Journal Info: Publisher: Taylor & Francis Country of Publication: England NLM ID: 101150203 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1475-6374 (Electronic) Linking ISSN: 14756366 NLM ISO Abbreviation: J Enzyme Inhib Med Chem Subsets: MEDLINE

MeSH Terms: Sequence Alignment* , Enzymes*/chemistry , Enzymes*/metabolism, Hydrophobic and Hydrophilic Interactions ; Amino Acid Sequence ; Autoencoder

SeqForge: a scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets.

Authors: Bring Horvath ER Winter JM

Source: BMC bioinformatics [BMC Bioinformatics] 2025 Nov 18; Vol. 26 (1), pp. 280. Date of Electronic Publication: 2025 Nov 18.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: Software* , Sequence Alignment*/methods , Genomics*/methods, Databases, Genetic ; Amino Acid Motifs ; Metagenomics/methods

KegAlign: optimizing pairwise alignments with diagonal partitioning.

Authors: Gulhan AB Burhans R Harris R et al.

Source: Genome biology [Genome Biol] 2025 Nov 17; Vol. 26 (1), pp. 389. Date of Electronic Publication: 2025 Nov 17.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE

MeSH Terms: Software* , Sequence Alignment*/methods , Genomics*/methods, Animals ; Humans ; Mice ; Algorithms

OneProt: Towards multi-modal protein foundation models via latent space alignment of sequence, structure, binding sites and text encoders.

Authors: Flöge K Udayakumar S Sommer J et al.

Source: PLoS computational biology [PLoS Comput Biol] 2025 Nov 13; Vol. 21 (11), pp. e1013679. Date of Electronic Publication: 2025 Nov 13 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Proteins*/metabolism , Sequence Alignment*/methods, Binding Sites ; Computational Biology/methods ; Deep Learning ; Neural Networks, Computer ; Sequence Analysis, Protein/methods ; Databases, Protein

DeepFold-PLM: accelerating protein structure prediction via efficient homology search using protein language models.

Authors: Kim M Bae H Jo G et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2025 Nov 01; Vol. 41 (11).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Software* , Sequence Alignment*/methods , Computational Biology*/methods, Protein Conformation ; Databases, Protein ; Models, Molecular ; Sequence Analysis, Protein/methods ; Algorithms

Training bias and sequence alignments shape protein-peptide docking by AlphaFold and related methods.

Authors: Guan L Keating AE

Source: Protein science : a publication of the Protein Society [Protein Sci] 2025 Nov; Vol. 34 (11), pp. e70331.

Publication Type: Journal Article

Journal Info: Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print Cited Medium: Internet ISSN: 1469-896X (Electronic) Linking ISSN: 09618368 NLM ISO Abbreviation: Protein Sci Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Proteins*/metabolism , Peptides*/chemistry , Peptides*/metabolism , Sequence Alignment*/methods , Molecular Docking Simulation*, Protein Binding ; Binding Sites ; Amino Acid Sequence ; Computational Biology/methods

PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences.

Authors: Pospelova M Safonova Y

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2025 Oct 02; Vol. 41 (10).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

MeSH Terms: Software* , Sequence Alignment*/methods, Computer Graphics

A novel pairwise sequence alignment algorithm for similarity search in massive datasets.

Authors: Masoudi-Sobhanzadeh Y Omidi Y

Source: Briefings in bioinformatics [Brief Bioinform] 2025 Aug 31; Vol. 26 (5).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

MeSH Terms: Algorithms* , Sequence Alignment*/methods , Sequence Alignment*/statistics & numerical data, Computational Biology/methods ; Software

Distant Homology BLASTP Searches.

Authors: Dwyer DS; Departments of Psychiatry and Behavioral Medicine and Pharmacology, Toxicology and Neuroscience, LSU Health Shreveport, Shreveport, LA, USA. donard.dwyer@lsuhs.edu.

Source: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2026; Vol. 2979, pp. 3-16.

Publication Type: Journal Article

Journal Info: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE

MeSH Terms: Sequence Alignment*/methods , Computational Biology*/methods, Animals ; Neuropeptides/genetics ; Neuropeptides/chemistry ; Islet Amyloid Polypeptide/genetics ; Islet Amyloid Polypeptide/chemistry ; Caenorhabditis elegans/genetics ; Kisspeptins/genetics ; Kisspeptins/chemistry ; Amino Acid Sequence ; Software

Detection of Specificity-Determining Positions in Protein Families.

Authors: Pitarch B Juan D Pazos F

Source: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2026; Vol. 2979, pp. 49-63.

Publication Type: Journal Article

Journal Info: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Proteins*/genetics , Proteins*/metabolism , Sequence Alignment*/methods , Computational Biology*/methods, Software ; Sequence Analysis, Protein/methods ; Databases, Protein ; Amino Acid Sequence

SynchDP: A correlation based sequence alignment algorithm for synchronizing longitudinal clinical data.

Authors: Seong S Bae S Jang J et al.

Source: Computers in biology and medicine [Comput Biol Med] 2025 Sep; Vol. 196 (Pt C), pp. 110853. Date of Electronic Publication: 2025 Aug 17.

Publication Type: Journal Article

Journal Info: Publisher: Elsevier Country of Publication: United States NLM ID: 1250250 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1879-0534 (Electronic) Linking ISSN: 00104825 NLM ISO Abbreviation: Comput Biol Med Subsets: MEDLINE

MeSH Terms: Algorithms* , COVID-19*/genetics , Sequence Alignment*/methods , SARS-CoV-2*/genetics, Humans ; Longitudinal Studies ; Gene Expression Profiling

Aryana-bs: context-aware alignment of bisulfite-sequencing reads.

Authors: Nikaein H Sharifi-Zarchi A Afzal A et al.

Source: BMC bioinformatics [BMC Bioinformatics] 2025 Jul 21; Vol. 26 (1), pp. 188. Date of Electronic Publication: 2025 Jul 21.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: Sequence Analysis, DNA*/methods , Sulfites*/chemistry , Sequence Alignment*/methods , Software*, DNA Methylation ; Humans ; Algorithms

SARST2 high-throughput and resource-efficient protein structure alignment against massive databases.

Authors: Lo WC Warshel A Lo CH et al.

Source: Nature communications [Nat Commun] 2025 Sep 30; Vol. 16 (1), pp. 8691. Date of Electronic Publication: 2025 Sep 30.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

MeSH Terms: Databases, Protein* , Proteins*/chemistry , Software* , Computational Biology*/methods , Sequence Alignment*/methods, Algorithms ; Protein Conformation ; Machine Learning

Ten practical tips and tricks to improve the effectiveness of biological network alignment.

Authors: Agapito G Cannataro M Cinaglia P et al.

Source: PLoS computational biology [PLoS Comput Biol] 2025 Sep 04; Vol. 21 (9), pp. e1013386. Date of Electronic Publication: 2025 Sep 04 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

MeSH Terms: Computational Biology*/methods , Sequence Alignment*/methods, Animals ; Humans ; Algorithms

RabbitBAM: Accelerating BAM File Manipulation on Multi-Core Platforms.

Authors: Yan L Zhao Z Yin Z et al.

Source: IEEE transactions on computational biology and bioinformatics [IEEE Trans Comput Biol Bioinform] 2025 Sep-Oct; Vol. 22 (5), pp. 2320-2326.

Publication Type: Journal Article

Journal Info: Publisher: IEEE Country of Publication: United States NLM ID: 9919068173606676 Publication Model: Print Cited Medium: Internet ISSN: 2998-4165 (Electronic) Linking ISSN: 29984165 NLM ISO Abbreviation: IEEE Trans Comput Biol Bioinform Subsets: MEDLINE

MeSH Terms: High-Throughput Nucleotide Sequencing*/methods , Software* , Sequence Analysis, DNA*/methods , Computational Biology*/methods , Sequence Alignment*/methods, Humans

Panaln: indexing pangenome for read alignment.

Authors: Guo L He Z Huo H

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2025 Sep 01; Vol. 41 (9).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

MeSH Terms: Software* , Sequence Alignment*/methods , Genomics*/methods , Sequence Analysis, DNA*/methods, Algorithms ; Humans

Dotplotic: a lightweight visualization tool for BLAST + alignments and genomic annotations.

Authors: Miyazawa H Oda T

Source: BMC bioinformatics [BMC Bioinformatics] 2025 Aug 27; Vol. 26 (1), pp. 222. Date of Electronic Publication: 2025 Aug 27.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: Software* , Sequence Alignment*/methods , Genomics*/methods , Molecular Sequence Annotation*/methods, Algorithms ; Computational Biology/methods