Literature DB >> 33401773

4SpecID: Reference DNA Libraries Auditing and Annotation System for Forensic Applications.

Luís Neto1, Nádia Pinto2,3,4, Alberto Proença1,5, António Amorim2,3,6, Eduardo Conde-Sousa2,7.   

Abstract

Forensic genetics is a fast-growing field that frequently requires DNA-based taxonomy, namely, when evidence are parts of specimens, often highly processed in food, potions, or ointments. Reference DNA-sequences libraries, such as BOLD or GenBank, are imperative tools for taxonomic assignment, particularly when morphology is inadequate for classification. The auditing and curation of these datasets require reliable mechanisms, preferably with automated data preprocessing. Software tools were developed to grade these datasets considering as primary criterion the number of records, which is not compliant with forensic standards, where the priority is validation from independent sources. Moreover, 4SpecID is an efficient software tool developed to audit and annotate reference libraries, specifically designed for forensic applications. Its intuitive user-friendly interface virtually accesses any database and includes specific data mining functions tuned for the widespread BOLD repositories. The built tool was evaluated in laptop MacBook and a dual-Xeon server with a large BOLD dataset (Culicidae, 36,115 records), and the best execution time to grade the dataset on the laptop was 0.28 s. Datasets of Bovidae and Felidae families were used to evaluate the quality of the tool and the relevance of independent sources validation.

Entities:  

Keywords:  BOLD system; DNA; barcoding; database auditing; efficient software; forensics; genetics; species identification; taxonomy

Mesh:

Year:  2021        PMID: 33401773      PMCID: PMC7824288          DOI: 10.3390/genes12010061

Source DB:  PubMed          Journal:  Genes (Basel)        ISSN: 2073-4425            Impact factor:   4.096


  14 in total

1.  Phylogenomics and species delimitation for effective conservation of manta and devil rays.

Authors:  Jane Hosegood; Emily Humble; Rob Ogden; Mark de Bruyn; Simon Creer; Guy M W Stevens; Mohammed Abudaya; Kim Bassos-Hull; Ramon Bonfil; Daniel Fernando; Andrew D Foote; Helen Hipperson; Rima W Jabado; Jennifer Kaden; Muhammad Moazzam; Lauren R Peel; Stephen Pollett; Alessandro Ponzo; Marloes Poortvliet; Jehad Salah; Helen Senn; Joshua D Stewart; Sabine Wintner; Gary Carvalho
Journal:  Mol Ecol       Date:  2020-11-09       Impact factor: 6.185

2.  Species assignment in forensics and the challenge of hybrids.

Authors:  Antonio Amorim; Filipe Pereira; Cíntia Alves; Oscar García
Journal:  Forensic Sci Int Genet       Date:  2020-06-17       Impact factor: 4.882

3.  DNA Barcoding unveils cryptic lineages of Hoplias malabaricus from Northeastern Brazil.

Authors:  W M M Pires; M C Barros; E C Fraga
Journal:  Braz J Biol       Date:  2021-11-30       Impact factor: 1.651

4.  A ranking system for reference libraries of DNA barcodes: application to marine fish species from Portugal.

Authors:  Filipe O Costa; Monica Landi; Rogelia Martins; Maria H Costa; Maria E Costa; Miguel Carneiro; Maria J Alves; Dirk Steinke; Gary R Carvalho
Journal:  PLoS One       Date:  2012-04-25       Impact factor: 3.240

5.  R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring.

Authors:  Frédéric Rimet; Philippe Chaumeil; François Keck; Lenaïg Kermarrec; Valentin Vasselon; Maria Kahlert; Alain Franc; Agnès Bouchez
Journal:  Database (Oxford)       Date:  2016-03-17       Impact factor: 3.451

6.  GenBank.

Authors:  Dennis A Benson; Mark Cavanaugh; Karen Clark; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; Eric W Sayers
Journal:  Nucleic Acids Res       Date:  2016-11-28       Impact factor: 16.971

7.  The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.

Authors:  Rolf Henrik Nilsson; Karl-Henrik Larsson; Andy F S Taylor; Johan Bengtsson-Palme; Thomas S Jeppesen; Dmitry Schigel; Peter Kennedy; Kathryn Picard; Frank Oliver Glöckner; Leho Tedersoo; Irja Saar; Urmas Kõljalg; Kessy Abarenkov
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

8.  A DNA-based registry for all animal species: the barcode index number (BIN) system.

Authors:  Sujeevan Ratnasingham; Paul D N Hebert
Journal:  PLoS One       Date:  2013-07-08       Impact factor: 3.240

9.  GenBank.

Authors:  Dennis A Benson; Mark Cavanaugh; Karen Clark; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; Eric W Sayers
Journal:  Nucleic Acids Res       Date:  2012-11-27       Impact factor: 16.971

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