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Bioinformatics. 2016 Sep 15;32(18):2776-82. doi: 10.1093/bioinformatics/btw319. Epub 2016 Jun 9.

Revealing aperiodic aspects of solenoid proteins from sequence information.

Author information

1
Department of Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.

Abstract

MOTIVATION:

Repeat proteins, which contain multiple repeats of short sequence motifs, form a large but seldom-studied group of proteins. Methods focusing on the analysis of 3D structures of such proteins identified many subtle effects in length distribution of individual motifs that are important for their functions. However, similar analysis was yet not applied to the vast majority of repeat proteins with unknown 3D structures, mostly because of the extreme diversity of the underlying motifs and the resulting difficulty to detect those.

RESULTS:

We developed FAIT, a sequence-based algorithm for the precise assignment of individual repeats in repeat proteins and introduced a framework to classify and compare aperiodicity patterns for large protein families. FAIT extracts repeat positions by post-processing FFAS alignment matrices with image processing methods. On examples of proteins with Leucine Rich Repeat (LRR) domains and other solenoids like proteins, we show that the automated analysis with FAIT correctly identifies exact lengths of individual repeats based entirely on sequence information.

AVAILABILITY AND IMPLEMENTATION:

https://github.com/GodzikLab/FAIT CONTACT: adam@godziklab.org

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
27334472
PMCID:
PMC6169467
DOI:
10.1093/bioinformatics/btw319
[Indexed for MEDLINE]
Free PMC Article

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