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Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper

par Crauwels, Charlotte;Heidig, Sophie-Luise ;Díaz, Adrián;Vranken, Wim
Référence Bioinformatics, 40, 5, btae276
Publication Publié, 2024-05

Article révisé par les pairs

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Résumé :

Summary: SIMSApiper is a Nextflow pipeline that creates reliable, structure-informed MSAs of thousands of protein sequences 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.