EncoMPASS: an Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry

Aleksandrova, Antoniya A.; Sarti, Edoardo; Forrest, Lucy R.

doi:10.1101/391961

Cited by 4 publications

(4 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Another practical application would include the need for a full-length alignment of two sequences, but where only fragments of the alignment are available. The sources of such aligned fragments might include high-quality local alignments, or structural alignments of repeated elements within a structure, as in the case of membrane-protein symmetry analysis [48,49]. In such cases, it is desirable to have an unbiased, but computationally efficient, method by which to construct the remainder of the alignment while maintaining the exact matching for the fragment.…”

Section: Anchors For Ensuring Accuracy In Fragments Of Alignmentsmentioning

confidence: 99%

Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors

et al. 2021

Self Cite

View full text Add to dashboard Cite

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. 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. Frequently, biochemical or biophysical data is available that informs the optimum alignment, for example, indicating specific positions that share common functional or structural roles. 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. However, such modifications are problematic because they reduce the robustness and reproducibility of the aligned regions either side of the newly matched positions. Previous studies have introduced restraints as a means to impose the matching of positions during sequence alignments, originally in the context of genome assembly. 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. 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. Anchored alignments can be generated using the online version of AlignMe available at www.bioinfo.mpg.de/AlignMe/.

show abstract

Section: Anchors For Ensuring Accuracy In Fragments Of Alignmentsmentioning

confidence: 99%

Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…Another promising application of anchors is situations in which a full-length alignment of two sequences is required, but where only fragments of the alignment are available from other tools. Such sources of aligned fragments might include local alignments, or structural alignments of repeated elements within a structure, as in the case of membrane-protein symmetry analysis (Sarti et al 2018;Aleksandrova, Sarti, and Forrest 2018). In such cases, it is desirable to have an unbiased method by which to construct the remainder of the alignment.…”

Section: Assessment Of the Compounding Effects Of Anchorsmentioning

confidence: 99%

Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors

Staritzbichler

Sarti²,

Yaklich

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

The alignment of primary sequences is a fundamental step in the analysis of protein structure, function, and evolution. 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. Frequently, biochemical or biophysical data is available that informs the optimum alignment, for example, indicating specific positions that share common functional or structural roles. Currently, if those positions are not correctly aligned by a standard pairwise alignment procedure, the incorporation of such information into the alignment is typically addressed in an ad hoc manner, with manual adjustments. However, such modifications are problematic because they reduce the robustness and reproducibility of the alignment. An alternative approach is the use of restraints, or anchors, to incorporate such position-matching explicitly during alignment. Here we introduce position anchoring in the alignment tool AlignMe as an aid to pairwise sequence alignment of membrane proteins. Applying this approach to realistic scenarios involving distantly-related and low complexity sequences, we illustrate how the addition of even a single anchor can dramatically improve the accuracy of the alignments, while maintaining the reproducibility and rigor of the overall alignment.

show abstract

Section: Anchors For Ensuring Accuracy In Fragments Of Alignmentsmentioning

confidence: 99%

Untitled

View full text Add to dashboard Cite

EncoMPASS: an Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry

Cited by 4 publications

References 62 publications

Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors

Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors

Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors

Untitled

Contact Info

Product

Resources

About