GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

Sela, Itamar and Ashkenazy, Haim and Katoh, Kazutaka,(16 April 2015), GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. , Nucleic Acids Research,, UNSPECIFIED

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Abstract

Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. However, from the same set of sequences different MSAs are often inferred, depending on the methodologies used and the assumed parameters. Much effort has recently been devoted to improving the ability to identify unreliable alignment regions. Detecting such unreliable regions was previously shown to be important for downstream analyses relying on MSAs, such as the detection of positive selection. Here we developed GUIDANCE2, a new integrative methodology that accounts for: (i) uncertainty in the process of indel formation, (ii) uncertainty in the assumed guide tree and (iii) co-optimal solutions in the pairwise alignments, used as building blocks in progressive alignment algorithms. We compared GUIDANCE2 with seven methodologies to detect unreliable MSA regions using extensive simulations and empirical benchmarks. We show that GUIDANCE2 outperforms all previously developed methodologies. Furthermore, GUIDANCE2 also provides a set of alternative MSAs which can be useful for downstream analyses. The novel algorithm is implemented as a web-server, available at: http: //guidance.tau.ac.il.
Keywords : UNSPECIFIED, UNSPECIFIED
Journal or Publication Title: Nucleic Acids Research,
Volume: 43
Number: UNSPECIFIED
Item Type: Article
Subjects: Akuntansi
Depositing User: Gunawan Gunawan
Date Deposited: 26 Dec 2019 06:32
Last Modified: 26 Dec 2019 06:32
URI: https://repofeb.undip.ac.id/id/eprint/853

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