IsoAligner. Dynamic mapping of amino acid positions across protein isoforms
Autor:innen
Autor:in (Körperschaft)
Publikationsdatum
31.03.2022
Typ der Arbeit
Studiengang
Typ
01A - Beitrag in wissenschaftlicher Zeitschrift
Herausgeber:innen
Herausgeber:in (Körperschaft)
Betreuer:in
Übergeordnetes Werk
F1000Research
Themenheft
DOI der Originalpublikation
Reihe / Serie
Reihennummer
Jahrgang / Band
11
Ausgabe / Nummer
Seiten / Dauer
Patentnummer
Verlag / Herausgebende Institution
Faculty of 1000
Verlagsort / Veranstaltungsort
Auflage
Version
Programmiersprache
Abtretungsempfänger:in
Praxispartner:in/Auftraggeber:in
Zusammenfassung
Aligning protein isoform sequences is often performed in cancer diagnostics to homogenise mutation annotations from different diagnostic assays. However, most alignment tools are fitted for homologous sequences, leading often to alignments of non-identical exonic regions. Here, we present the interactive alignment webservice IsoAligner for exact mapping of exonic protein subsequences. The tool uses a customized Needleman-Wunsch algorithm including an open gap penalty combined with a gene-specific minimal exon length function and dynamically adjustable parameters. As an input, IsoAligner accepts either various gene/transcript/protein IDs from different databases (Ensembl, UniProt, RefSeq) or raw amino acid sequences. The output of IsoAligner consists of pairwise alignments and a table of mapped amino acid positions between the canonical or supplied isoform IDs and all alternative isoforms. IsoAligner’s human isoform library comprises of over 1.3 million IDs mapped on over 120,000 protein sequences. IsoAligner, is a fast and interactive alignment tool for retrieving amino acids positions between different protein isoforms. Its application will allow diagnostic and precision medicine labs to detect inconsistent variant annotations between different assays and databases. Availability: This tool is available as a Webservice on www.isoaligner.org. A REST API is available for programmatic access. The source code for both services can be found at https://github.com/mtp-usz/IsoAligner.
Schlagwörter
Alignment, Protein isoform, Amino acid sequence, Protein ids, Exon-mapping
Fachgebiet (DDC)
600 - Technik, Medizin, angewandte Wissenschaften
Veranstaltung
Startdatum der Ausstellung
Enddatum der Ausstellung
Startdatum der Konferenz
Enddatum der Konferenz
Datum der letzten Prüfung
ISBN
ISSN
2046-1402
Sprache
Englisch
Während FHNW Zugehörigkeit erstellt
Nein
Zukunftsfelder FHNW
Publikationsstatus
Preprint
Begutachtung
Peer-Review der ganzen Publikation
Open Access-Status
Green
Lizenz
Zitation
HANIMANN, Jacob, Holger MOCH, Martin ZOCHE und Abdullah KAHRAMAN, 2022. IsoAligner. Dynamic mapping of amino acid positions across protein isoforms. F1000Research. 31 März 2022. Bd. 11. DOI 10.12688/f1000research.76154.1. Verfügbar unter: https://doi.org/10.26041/fhnw-4838