Large-scale Structure-Informed multiple sequence alignment of proteins with SIMSApiper

Charlotte Crauwels; Sophie-Luise Heidig; Adrián Díaz; Wim Vranken

doi:10.1093/bioinformatics/btae276

Large-scale Structure-Informed multiple sequence alignment of proteins with SIMSApiper

Charlotte Crauwels, Sophie-Luise Heidig, Adrián Díaz, Wim Vranken

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Abstract

SIMSApiper is a Nextflow pipeline that creates reliable, structure-informed MSAs of thousands of protein sequences in time-frames faster than standard structure-based alignment methods. Structural information can be provided by the user or collected by the pipeline from online resources. Parallelization with sequence identity based subsets can be activated to significantly speed up the alignment process. Finally, the number of gaps in the final alignment can be reduced by leveraging the position of conserved secondary structure elements.

Original language	English
Article number	btae276
Number of pages	5
Journal	Bioinformatics
Volume	40
Issue number	5
DOIs	https://doi.org/10.1093/bioinformatics/btae276
Publication status	Published - 22 Apr 2024

Bibliographical note

Funding Information:
This work was supported by Research Foundation Flanders (FWO) SB PhD fellowship [1SE5923N] to C.C.; the FWO large infrastructure grant [I000323N] to A.D.; and the Fonds de la Recherche Scientifique (FNRS) Aspirant fellowship to S.L.H. The resources used in this work were provided in part by the VSC (Flemish Supercomputer Center), funded by the Research Foundation\u2014Flanders (FWO) and the Flemish Government.

Publisher Copyright:
© 2024 The Author(s). Published by Oxford University Press.

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Cite this

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Large-scale Structure-Informed multiple sequence alignment of proteins with SIMSApiper

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