Mathilde Carpentier1, Jacques Chomilier2. 1. Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France. 2. Sorbonne Université, MNHN, CNRS, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), BiBiP, Paris, France.
Abstract
MOTIVATION: Multiple sequence alignment programs have proved to be very useful and have already been evaluated in the literature yet not alignment programs based on structure or both sequence and structure. In the present article we wish to evaluate the added value provided through considering structures. RESULTS: We compared the multiple alignments resulting from 25 programs either based on sequence, structure or both, to reference alignments deposited in five databases (BALIBASE 2 and 3, HOMSTRAD, OXBENCH and SISYPHUS). On the whole, the structure-based methods compute more reliable alignments than the sequence-based ones, and even than the sequence+structure-based programs whatever the databases. Two programs lead, MAMMOTH and MATRAS, nevertheless the performances of MUSTANG, MATT, 3DCOMB, TCOFFEE+TM_ALIGN and TCOFFEE+SAP are better for some alignments. The advantage of structure-based methods increases at low levels of sequence identity, or for residues in regular secondary structures or buried ones. Concerning gap management, sequence-based programs set less gaps than structure-based programs. Concerning the databases, the alignments of the manually built databases are more challenging for the programs. AVAILABILITY AND IMPLEMENTATION: All data and results presented in this study are available at: http://wwwabi.snv.jussieu.fr/people/mathilde/download/AliMulComp/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Multiple sequence alignment programs have proved to be very useful and have already been evaluated in the literature yet not alignment programs based on structure or both sequence and structure. In the present article we wish to evaluate the added value provided through considering structures. RESULTS: We compared the multiple alignments resulting from 25 programs either based on sequence, structure or both, to reference alignments deposited in five databases (BALIBASE 2 and 3, HOMSTRAD, OXBENCH and SISYPHUS). On the whole, the structure-based methods compute more reliable alignments than the sequence-based ones, and even than the sequence+structure-based programs whatever the databases. Two programs lead, MAMMOTH and MATRAS, nevertheless the performances of MUSTANG, MATT, 3DCOMB, TCOFFEE+TM_ALIGN and TCOFFEE+SAP are better for some alignments. The advantage of structure-based methods increases at low levels of sequence identity, or for residues in regular secondary structures or buried ones. Concerning gap management, sequence-based programs set less gaps than structure-based programs. Concerning the databases, the alignments of the manually built databases are more challenging for the programs. AVAILABILITY AND IMPLEMENTATION: All data and results presented in this study are available at: http://wwwabi.snv.jussieu.fr/people/mathilde/download/AliMulComp/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Jennifer T Vu; Elena Wang; Jolan Wu; Young Joo Sun; Gabriel Velez; Alexander G Bassuk; Soo Hyeon Lee; Vinit B Mahajan Journal: Trends Mol Med Date: 2022-05-29 Impact factor: 15.272
Authors: Gabriel Velez; Young Joo Sun; Saif Khan; Jing Yang; Jonathan Herrmann; Teja Chemudupati; Robert E MacLaren; Lokesh Gakhar; Soichi Wakatsuki; Alexander G Bassuk; Vinit B Mahajan Journal: Cell Rep Date: 2020-01-21 Impact factor: 9.423