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A web-based platform of nucleotide sequence alignments of plants

Chiara Santos, View ORCID ProfileJoão Carneiro, View ORCID ProfileFilipe Pereira
doi: https://doi.org/10.1101/617035
Chiara Santos
1Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões; Avenida General Norton de Matos, S/N 4450-208 Matosinhos – Portugal
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João Carneiro
1Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões; Avenida General Norton de Matos, S/N 4450-208 Matosinhos – Portugal
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Filipe Pereira
2University of Porto, Praça Gomes Teixeira 4099-002 Porto, Portugal
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  • For correspondence: fpereirapt@gmail.com
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Abstract

In recent years, a large number of nucleotide sequences have become available for plant species by the advent of massive parallel sequencing. The use of genomic data has been important for agriculture, food science, medicine or ecology. Despite the increasing amount of data, nucleotide sequences are usually available in public databases as isolated records with some descriptive information. Researchers interested in studying a wide range of specific plant families are forced to do multiple searches, sequence downloads, data curation and sequence alignments. In order to help researches overcoming these problems, we have built a comprehensive on-line resource of curated nucleotide sequence alignments for plant research, named PlantAligDB (available at http://plantaligdb.portugene.com). The latest release incorporates 514 alignments with a total of 66,052 sequences from six important genomic regions: atpF-atpH, psbA-trnH, trnL, rbcL, matK and ITS. The alignments represent 223 plant families from a variety of taxonomic groups. The users can quickly search the database, download and visualize the curated alignments and phylogenetic trees using dynamic browser-based applications. Different measures of genetic diversity are also available for each plant family. We also provide the workflow script that allows the user to do the curation process, explaining the steps involved. Overall, the PlantAligDB provides a complete, quality checked and regularly updated collection of alignments that can be used in taxonomic, DNA barcoding, molecular genetics, phylogenetic and evolutionary studies.

Footnotes

  • Acknowledgments were updated.

  • http://plantaligdb.portugene.com/cgi-bin/PlantAligDB_home.cgi

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 02, 2019.
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A web-based platform of nucleotide sequence alignments of plants
Chiara Santos, João Carneiro, Filipe Pereira
bioRxiv 617035; doi: https://doi.org/10.1101/617035
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A web-based platform of nucleotide sequence alignments of plants
Chiara Santos, João Carneiro, Filipe Pereira
bioRxiv 617035; doi: https://doi.org/10.1101/617035

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