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https://doi.org/10.21256/zhaw-23747| Publikationstyp: | Beitrag in wissenschaftlicher Zeitschrift |
| Art der Begutachtung: | Peer review (Publikation) |
| Titel: | ProPIP : a tool for progressive multiple sequence alignment with Poisson Indel Process |
| Autor/-in: | Maiolo, Massimo Gatti, Lorenzo Frei, Diego Leidi, Tiziano Gil, Manuel Anisimova, Maria |
| et. al: | No |
| DOI: | 10.1186/s12859-021-04442-8 10.21256/zhaw-23747 |
| Erschienen in: | BMC Bioinformatics |
| Band(Heft): | 22 |
| Heft: | 1 |
| Seite(n): | 518 |
| Erscheinungsdatum: | 24-Okt-2021 |
| Verlag / Hrsg. Institution: | BioMed Central |
| ISSN: | 1471-2105 |
| Sprache: | Englisch |
| Schlagwörter: | Alignment software; Dynamic programming; Evolutionary alignment; Indel evolution; Multiple sequence alignmnet; Poisson Indel Process; Algorithm; Phylogeny; Sequence alignment; Software; Evolution, molecular; INDEL mutation |
| Fachgebiet (DDC): | 005: Computerprogrammierung, Programme und Daten |
| Zusammenfassung: | Background Current alignment tools typically lack an explicit model of indel evolution, leading to artificially short inferred alignments (i.e., over-alignment) due to inconsistencies between the indel history and the phylogeny relating the input sequences. Results We present a new progressive multiple sequence alignment tool ProPIP. The process of insertions and deletions is described using an explicit evolutionary model—the Poisson Indel Process or PIP. The method is based on dynamic programming and is implemented in a frequentist framework. The source code can be compiled on Linux, macOS and Microsoft Windows platforms. The algorithm is implemented in C++ as standalone program. The source code is freely available on GitHub at https://github.com/acg-team/ProPIP and is distributed under the terms of the GNU GPL v3 license. Conclusions The use of an explicit indel evolution model allows to avoid over-alignment, to infer gaps in a phylogenetically consistent way and to make inferences about the rates of insertions and deletions. Instead of the arbitrary gap penalties, the parameters used by ProPIP are the insertion and deletion rates, which have biological interpretation and are contextualized in a probabilistic environment. As a result, indel rate settings may be optimised in order to infer phylogenetically meaningful gap patterns. |
| URI: | https://digitalcollection.zhaw.ch/handle/11475/23747 |
| Volltext Version: | Publizierte Version |
| Lizenz (gemäss Verlagsvertrag): | CC BY 4.0: Namensnennung 4.0 International |
| Departement: | Life Sciences und Facility Management |
| Organisationseinheit: | Institut für Computational Life Sciences (ICLS) |
| Publiziert im Rahmen des ZHAW-Projekts: | Fast joint estimation of alignment and phylogeny from genomics sequences in a frequentist framework |
| Enthalten in den Sammlungen: | Publikationen Life Sciences und Facility Management |
Dateien zu dieser Ressource:
| Datei | Beschreibung | Größe | Format | |
|---|---|---|---|---|
| 2021_Maiolo-etal_ProPIP_BMC-Bioinformatics.pdf | 2.19 MB | Adobe PDF |  Öffnen/Anzeigen |
Zur Langanzeige
Maiolo, M., Gatti, L., Frei, D., Leidi, T., Gil, M., & Anisimova, M. (2021). ProPIP : a tool for progressive multiple sequence alignment with Poisson Indel Process. BMC Bioinformatics, 22(1), 518. https://doi.org/10.1186/s12859-021-04442-8
Maiolo, M. et al. (2021) ‘ProPIP : a tool for progressive multiple sequence alignment with Poisson Indel Process’, BMC Bioinformatics, 22(1), p. 518. Available at: https://doi.org/10.1186/s12859-021-04442-8.
M. Maiolo, L. Gatti, D. Frei, T. Leidi, M. Gil, and M. Anisimova, “ProPIP : a tool for progressive multiple sequence alignment with Poisson Indel Process,” BMC Bioinformatics, vol. 22, no. 1, p. 518, Oct. 2021, doi: 10.1186/s12859-021-04442-8.
MAIOLO, Massimo, Lorenzo GATTI, Diego FREI, Tiziano LEIDI, Manuel GIL und Maria ANISIMOVA, 2021. ProPIP : a tool for progressive multiple sequence alignment with Poisson Indel Process. BMC Bioinformatics. 24 Oktober 2021. Bd. 22, Nr. 1, S. 518. DOI 10.1186/s12859-021-04442-8
Maiolo, Massimo, Lorenzo Gatti, Diego Frei, Tiziano Leidi, Manuel Gil, and Maria Anisimova. 2021. “ProPIP : A Tool for Progressive Multiple Sequence Alignment with Poisson Indel Process.” BMC Bioinformatics 22 (1): 518. https://doi.org/10.1186/s12859-021-04442-8.
Maiolo, Massimo, et al. “ProPIP : A Tool for Progressive Multiple Sequence Alignment with Poisson Indel Process.” BMC Bioinformatics, vol. 22, no. 1, Oct. 2021, p. 518, https://doi.org/10.1186/s12859-021-04442-8.
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