A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Brief Communication: Foldable subunits of helix protein
Computational Biology and Chemistry
Latent periodicity of serine-threonine and tyrosine protein kinases and other protein families
Computational Biology and Chemistry
Gapped extension for local multiple alignment of interspersed DNA repeats
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Procrastination leads to efficient filtration for local multiple alignment
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Detecting fuzzy amino acid tandem repeats in protein sequences
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Research Article: Analysis of sequence repeats of proteins in the PDB
Computational Biology and Chemistry
| Hi-index | 3.84 |
Motivation: Internal repeats in coding sequences correspond to structural and functional units of proteins. Moreover, duplication of fragments of coding sequences is known to be a mechanism to facilitate evolution. Identification of repeats is crucial to shed light on the function and structure of proteins, and explain their evolutionary past. The task is difficult because during the course of evolution many repeats diverged beyond recognition. Results: We introduce a new method TRUST, for ab initio determination of internal repeats in proteins. It provides an improvement in prediction quality as compared to alternative state-of-the-art methods. The increased sensitivity and accuracy of the method is achieved by exploiting the concept of transitivity of alignments. Starting from significant local suboptimal alignments, the application of transitivity allows us to (1) identify distant repeat homologues for which no alignments were found; (2) gain confidence about consistently well-aligned regions; and (3) recognize and reduce the contribution of non-homologous repeats. This re-assessment step enables us to derive a virtually noise-free profile representing a generalized repeat with high fidelity. We also obtained superior specificity by employing rigid statistical testing for self-sequence and profile-sequence alignments. Assessment was done using a database of repeat annotations based on structural superpositioning. The results show that TRUST is a useful and reliable tool for mining tandem and non-tandem repeats in protein sequence databases, capable of predicting multiple repeat types with varying intervening segments within a single sequence. Availability: The TRUST server (together with the source code) is available at http://ibivu.cs.vu.nl/programs/trustwww