Exploring the adenylation domain repertoire of nonribosomal peptide synthetases using an ensemble of sequence-search methods.
The introduction of two-dimension (2D) graphs and their numerical characterization for comparative analyses of DNA/RNA and protein sequences without the need of sequence alignments is an active yet recent research topic in bioinformatics. Here, we used a 2D artificial representation (four-color maps...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3712989?pdf=render |
| _version_ | 1819060218575716352 |
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| author | Guillermin Agüero-Chapin Reinaldo Molina-Ruiz Emanuel Maldonado Gustavo de la Riva Aminael Sánchez-Rodríguez Vitor Vasconcelos Agostinho Antunes |
| author_facet | Guillermin Agüero-Chapin Reinaldo Molina-Ruiz Emanuel Maldonado Gustavo de la Riva Aminael Sánchez-Rodríguez Vitor Vasconcelos Agostinho Antunes |
| author_sort | Guillermin Agüero-Chapin |
| collection | DOAJ |
| description | The introduction of two-dimension (2D) graphs and their numerical characterization for comparative analyses of DNA/RNA and protein sequences without the need of sequence alignments is an active yet recent research topic in bioinformatics. Here, we used a 2D artificial representation (four-color maps) with a simple numerical characterization through topological indices (TIs) to aid the discovering of remote homologous of Adenylation domains (A-domains) from the Nonribosomal Peptide Synthetases (NRPS) class in the proteome of the cyanobacteria Microcystis aeruginosa. Cyanobacteria are a rich source of structurally diverse oligopeptides that are predominantly synthesized by NPRS. Several A-domains share amino acid identities lower than 20 % being a possible source of remote homologous. Therefore, A-domains cannot be easily retrieved by BLASTp searches using a single template. To cope with the sequence diversity of the A-domains we have combined homology-search methods with an alignment-free tool that uses protein four-color-maps. TI2BioP (Topological Indices to BioPolymers) version 2.0, available at http://ti2biop.sourceforge.net/ allowed the calculation of simple TIs from the protein sequences (four-color maps). Such TIs were used as input predictors for the statistical estimations required to build the alignment-free models. We concluded that the use of graphical/numerical approaches in cooperation with other sequence search methods, like multi-templates BLASTp and profile HMM, can give the most complete exploration of the repertoire of highly diverse protein families. |
| first_indexed | 2024-12-21T14:23:30Z |
| format | Article |
| id | doaj.art-d3a649b6e8a246d0bfeaef82c051581f |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-21T14:23:30Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-d3a649b6e8a246d0bfeaef82c051581f2022-12-21T19:00:43ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0187e6592610.1371/journal.pone.0065926Exploring the adenylation domain repertoire of nonribosomal peptide synthetases using an ensemble of sequence-search methods.Guillermin Agüero-ChapinReinaldo Molina-RuizEmanuel MaldonadoGustavo de la RivaAminael Sánchez-RodríguezVitor VasconcelosAgostinho AntunesThe introduction of two-dimension (2D) graphs and their numerical characterization for comparative analyses of DNA/RNA and protein sequences without the need of sequence alignments is an active yet recent research topic in bioinformatics. Here, we used a 2D artificial representation (four-color maps) with a simple numerical characterization through topological indices (TIs) to aid the discovering of remote homologous of Adenylation domains (A-domains) from the Nonribosomal Peptide Synthetases (NRPS) class in the proteome of the cyanobacteria Microcystis aeruginosa. Cyanobacteria are a rich source of structurally diverse oligopeptides that are predominantly synthesized by NPRS. Several A-domains share amino acid identities lower than 20 % being a possible source of remote homologous. Therefore, A-domains cannot be easily retrieved by BLASTp searches using a single template. To cope with the sequence diversity of the A-domains we have combined homology-search methods with an alignment-free tool that uses protein four-color-maps. TI2BioP (Topological Indices to BioPolymers) version 2.0, available at http://ti2biop.sourceforge.net/ allowed the calculation of simple TIs from the protein sequences (four-color maps). Such TIs were used as input predictors for the statistical estimations required to build the alignment-free models. We concluded that the use of graphical/numerical approaches in cooperation with other sequence search methods, like multi-templates BLASTp and profile HMM, can give the most complete exploration of the repertoire of highly diverse protein families.http://europepmc.org/articles/PMC3712989?pdf=render |
| spellingShingle | Guillermin Agüero-Chapin Reinaldo Molina-Ruiz Emanuel Maldonado Gustavo de la Riva Aminael Sánchez-Rodríguez Vitor Vasconcelos Agostinho Antunes Exploring the adenylation domain repertoire of nonribosomal peptide synthetases using an ensemble of sequence-search methods. PLoS ONE |
| title | Exploring the adenylation domain repertoire of nonribosomal peptide synthetases using an ensemble of sequence-search methods. |
| title_full | Exploring the adenylation domain repertoire of nonribosomal peptide synthetases using an ensemble of sequence-search methods. |
| title_fullStr | Exploring the adenylation domain repertoire of nonribosomal peptide synthetases using an ensemble of sequence-search methods. |
| title_full_unstemmed | Exploring the adenylation domain repertoire of nonribosomal peptide synthetases using an ensemble of sequence-search methods. |
| title_short | Exploring the adenylation domain repertoire of nonribosomal peptide synthetases using an ensemble of sequence-search methods. |
| title_sort | exploring the adenylation domain repertoire of nonribosomal peptide synthetases using an ensemble of sequence search methods |
| url | http://europepmc.org/articles/PMC3712989?pdf=render |
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