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Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences

The aim of this work was to compare the multiple alignment methods MAHDS, T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK in their ability to align highly divergent amino acid sequences. To accomplish this, we created test amino acid sequences with an average number of substitutions per am...

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Autores principales: Kostenko, Dimitrii O., Korotkov, Eugene V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8998981/
https://www.ncbi.nlm.nih.gov/pubmed/35409125
http://dx.doi.org/10.3390/ijms23073764
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author Kostenko, Dimitrii O.
Korotkov, Eugene V.
author_facet Kostenko, Dimitrii O.
Korotkov, Eugene V.
author_sort Kostenko, Dimitrii O.
collection PubMed
description The aim of this work was to compare the multiple alignment methods MAHDS, T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK in their ability to align highly divergent amino acid sequences. To accomplish this, we created test amino acid sequences with an average number of substitutions per amino acid (x) from 0.6 to 5.6, a total of 81 sets. Comparison of the performance of sequence alignments constructed by MAHDS and previously developed algorithms using the CS and Z score criteria and the benchmark alignment database (BAliBASE) indicated that, although the quality of the alignments built with MAHDS was somewhat lower than that of the other algorithms, it was compensated by greater statistical significance. MAHDS could construct statistically significant alignments of artificial sequences with x ≤ 4.8, whereas the other algorithms (T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK) could not perform that at x > 2.4. The application of MAHDS to align 21 families of highly diverged proteins (identity < 20%) from Pfam and HOMSTRAD databases showed that it could calculate statistically significant alignments in cases when the other methods failed. Thus, MAHDS could be used to construct statistically significant multiple alignments of highly divergent protein sequences, which accumulated multiple mutations during evolution.
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spelling pubmed-89989812022-04-12 Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences Kostenko, Dimitrii O. Korotkov, Eugene V. Int J Mol Sci Article The aim of this work was to compare the multiple alignment methods MAHDS, T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK in their ability to align highly divergent amino acid sequences. To accomplish this, we created test amino acid sequences with an average number of substitutions per amino acid (x) from 0.6 to 5.6, a total of 81 sets. Comparison of the performance of sequence alignments constructed by MAHDS and previously developed algorithms using the CS and Z score criteria and the benchmark alignment database (BAliBASE) indicated that, although the quality of the alignments built with MAHDS was somewhat lower than that of the other algorithms, it was compensated by greater statistical significance. MAHDS could construct statistically significant alignments of artificial sequences with x ≤ 4.8, whereas the other algorithms (T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK) could not perform that at x > 2.4. The application of MAHDS to align 21 families of highly diverged proteins (identity < 20%) from Pfam and HOMSTRAD databases showed that it could calculate statistically significant alignments in cases when the other methods failed. Thus, MAHDS could be used to construct statistically significant multiple alignments of highly divergent protein sequences, which accumulated multiple mutations during evolution. MDPI 2022-03-29 /pmc/articles/PMC8998981/ /pubmed/35409125 http://dx.doi.org/10.3390/ijms23073764 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Kostenko, Dimitrii O.
Korotkov, Eugene V.
Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences
title Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences
title_full Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences
title_fullStr Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences
title_full_unstemmed Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences
title_short Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences
title_sort application of the mahds method for multiple alignment of highly diverged amino acid sequences
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8998981/
https://www.ncbi.nlm.nih.gov/pubmed/35409125
http://dx.doi.org/10.3390/ijms23073764
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