9/27/2023 0 Comments Two protein sequence alignment![]() ![]() The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist.Ĭomparison of protein primary sequences is a fundamental step in analyzing evolutionary relationships and for accurate structural modeling based on homology. The work is made available under the Creative Commons CC0 public domain dedication.ĭata Availability: The data associated with the manuscript is now available on zenodo: with the following DOI: 10.5281/zenodo.4016927.įunding: This research was supported by the Division of Intramural Research of the NIH, National Institute of Neurological Disorders and Stroke Z00-NS003143 (LRF ) and by the Max Planck Gesellschaft (LRF ). This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. Received: SeptemAccepted: ApPublished: April 30, 2021 PLoS ONE 16(4):Įditor: Frederique Lisacek, Swiss Institute of Bioinformatics, SWITZERLAND (2021) Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors. Anchored alignments can be generated using the online version of AlignMe available at Citation: Staritzbichler R, Sarti E, Yaklich E, Aleksandrova A, Stamm M, Khafizov K, et al. Applying this approach to realistic scenarios involving distantly-related and low complexity sequences, we illustrate how the addition of anchors can be used to modify alignments, while still maintaining the reproducibility and rigor of the rest of the alignment. Here we introduce position restraints, or “anchors” as a feature in our alignment tool AlignMe, providing an aid to pairwise global sequence alignment of alpha-helical membrane proteins. Previous studies have introduced restraints as a means to impose the matching of positions during sequence alignments, originally in the context of genome assembly. However, such modifications are problematic because they reduce the robustness and reproducibility of the aligned regions either side of the newly matched positions. Currently, if those positions are not correctly matched by a standard pairwise sequence alignment procedure, the incorporation of such information into the alignment is typically addressed in an ad hoc manner, with manual adjustments. Frequently, biochemical or biophysical data is available that informs the optimum alignment, for example, indicating specific positions that share common functional or structural roles. Integral membrane proteins pose a significant challenge for such sequence alignment approaches, because their evolutionary relationships can be very remote, and because a high content of hydrophobic amino acids reduces their complexity. The alignment of primary sequences is a fundamental step in the analysis of protein structure, function, and evolution, and in the generation of homology-based models. ![]()
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