Search Results - "Sequence alignment"

A local sequence alignment approach to recognizing fixed poetic forms across languages.

Authors: Plecháč P Šeļa A

Source: PloS one [PLoS One] 2026 Jul 14; Vol. 21 (7), pp. e0340514. Date of Electronic Publication: 2026 Jul 14 (Print Publication: 2026).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

A-liner: linear alignment visualizer for genome comparisons.

Authors: Okuno M Yamamoto T Ogura Y et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 Jun 01; Vol. 42 (6).

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

Lift&Add-rapid and robust addition of new species to alignments of conserved non-coding sequences.

Authors: Shukla N Gallego Romero I

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 Jun 01; Vol. 42 (6).

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

NEFFy: a versatile tool for computing the number of effective sequences.

Authors: Haghani M Bhattacharya D Murali TM

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 Jun 01; Vol. 42 (6).

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

EMERALD-UI: an interactive web application to unveil novel protein biology hidden in the alternative alignment space.

Authors: Preoteasa A Grigorjew A Tomescu AI et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 May 03; Vol. 42 (5).

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

Singletrack: an algorithm for improving memory consumption and performance of gap-affine sequence alignment.

Authors: López-Villellas L Iñiguez C Jiménez-Blanco A et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 May 03; Vol. 42 (5).

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

Much ado about nothing: modeling amino acid replacement with predicted protein structures.

Authors: Buschmann L Bolz SN El-Hendi F et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 May 03; Vol. 42 (5).

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

BABAPPAlign: a multiple sequence alignment engine with a learned residue-level scoring function.

Authors: Sinha K; Department of Zoology, Jhargram Raj College, Jhargram, West Bengal 721507, India.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 May 03; Vol. 42 (5).

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

AliFilter: a machine learning approach to alignment filtering.

Authors: Bianchini G Zhu R Cicconardi F et al.

Source: Molecular biology and evolution [Mol Biol Evol] 2026 Apr 01; Vol. 43 (4).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: United States NLM ID: 8501455 Publication Model: Print Cited Medium: Internet ISSN: 1537-1719 (Electronic) Linking ISSN: 07374038 NLM ISO Abbreviation: Mol Biol Evol Subsets: MEDLINE

RECUR: identifying recurrent amino acid substitutions from multiple sequence alignments.

Authors: Robbins EHJ Liu Y Kelly S

Source: Molecular biology and evolution [Mol Biol Evol] 2026 Feb 02; Vol. 43 (2).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: United States NLM ID: 8501455 Publication Model: Print Cited Medium: Internet ISSN: 1537-1719 (Electronic) Linking ISSN: 07374038 NLM ISO Abbreviation: Mol Biol Evol Subsets: MEDLINE

Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches.

Authors: Wall BPG Ogata JD Nguyen M et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 Feb 28; Vol. 42 (3).

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

Accelerating minimap2 for whole-genome alignment.

Authors: Chandra G Vasimuddin M Misra S et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 Feb 28; Vol. 42 (3).

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

Inferring context-specific site variation with evotuned protein language models.

Authors: Lytras S Strange A Ito J et al.

Source: NAR genomics and bioinformatics [NAR Genom Bioinform] 2026 Feb 09; Vol. 8 (1), pp. lqag018. Date of Electronic Publication: 2026 Feb 09 (Print Publication: 2026).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 101756213 Publication Model: eCollection Cited Medium: Internet ISSN: 2631-9268 (Electronic) Linking ISSN: 26319268 NLM ISO Abbreviation: NAR Genom Bioinform Subsets: MEDLINE

Multiple protein structure alignment at scale with FoldMason.

Authors: Gilchrist CLM Mirdita M Steinegger M

Source: Science (New York, N.Y.) [Science] 2026 Jan 29; Vol. 391 (6784), pp. 485-488. Date of Electronic Publication: 2026 Jan 29.

Publication Type: Journal Article

Journal Info: Publisher: American Association for the Advancement of Science Country of Publication: United States NLM ID: 0404511 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1095-9203 (Electronic) Linking ISSN: 00368075 NLM ISO Abbreviation: Science Subsets: MEDLINE

Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments.

Authors: Malik AJ Mao S Hugenholtz P et al.

Source: Genome biology and evolution [Genome Biol Evol] 2026 Jan 02; Vol. 18 (1).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 101509707 Publication Model: Print Cited Medium: Internet ISSN: 1759-6653 (Electronic) Linking ISSN: 17596653 NLM ISO Abbreviation: Genome Biol Evol Subsets: MEDLINE

Alignoth: portable and interactive visualization of read alignments.

Authors: Wiegand F Mölder F Köster J

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 Jan 02; Vol. 42 (1).

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

SAFARI: pangenome alignment of ancient DNA using purine/pyrimidine encodings.

Authors: Rubin J van Waaij J Kraft L et al.

Source: NAR genomics and bioinformatics [NAR Genom Bioinform] 2025 Dec 10; Vol. 7 (4), pp. lqaf170. Date of Electronic Publication: 2025 Dec 10 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 101756213 Publication Model: eCollection Cited Medium: Internet ISSN: 2631-9268 (Electronic) Linking ISSN: 26319268 NLM ISO Abbreviation: NAR Genom Bioinform Subsets: MEDLINE

Columba: fast approximate pattern matching with optimized search schemes.

Authors: Renders L Depuydt L Gagie T et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2025 Dec 01; Vol. 41 (12).

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

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

T-shaped alignments integrating HIV-1 near full-length genome and partial pol sequences can improve phylogenetic inference of transmission clusters.

Authors: Guang A Dunn CW Novitsky V et al.

Source: PLoS computational biology [PLoS Comput Biol] 2025 Nov 25; Vol. 21 (11), pp. e1013676. Date of Electronic Publication: 2025 Nov 25 (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