USAT: a bioinformatic toolkit to facilitate interpretation and comparative visualization of tandem repeat sequences.
Allele comparison
DNA
Forensics STR
Genome comparison
Haplotype
Tandem repeat
Journal
BMC bioinformatics
ISSN: 1471-2105
Titre abrégé: BMC Bioinformatics
Pays: England
ID NLM: 100965194
Informations de publication
Date de publication:
19 Nov 2022
19 Nov 2022
Historique:
received:
10
05
2022
accepted:
29
10
2022
entrez:
19
11
2022
pubmed:
20
11
2022
medline:
23
11
2022
Statut:
epublish
Résumé
Tandem repeats (TR), highly variable genomic variants, are widely used in individual identification, disease diagnostics, and evolutionary studies. The recent advances in sequencing technologies and bioinformatic tools facilitate calling TR haplotypes genome widely. Both length-based and sequence-based TR alleles are used in different applications. However, sequence-based TR alleles could provide the highest precision in characterizing TR haplotypes. The need to identify the differences at the single nucleotide level between or among TR haplotypes with an easy-use bioinformatic tool is essential. In this study, we developed a Universal STR Allele Toolkit (USAT) for TR haplotype analysis, which takes TR haplotype output from existing tools to perform allele size conversion, sequence comparison of haplotypes, figure plotting, comparison for allele distribution, and interactive visualization. An exemplary application of USAT for analysis of the CODIS core STR loci for DNA forensics with benchmarking human individuals demonstrated the capabilities of USAT. USAT has user-friendly graphic interfaces and runs fast in major computing operating systems with parallel computing enabled. USAT is a user-friendly bioinformatics software for interpretation, visualization, and comparisons of TRs.
Sections du résumé
BACKGROUND
BACKGROUND
Tandem repeats (TR), highly variable genomic variants, are widely used in individual identification, disease diagnostics, and evolutionary studies. The recent advances in sequencing technologies and bioinformatic tools facilitate calling TR haplotypes genome widely. Both length-based and sequence-based TR alleles are used in different applications. However, sequence-based TR alleles could provide the highest precision in characterizing TR haplotypes. The need to identify the differences at the single nucleotide level between or among TR haplotypes with an easy-use bioinformatic tool is essential.
RESULTS
RESULTS
In this study, we developed a Universal STR Allele Toolkit (USAT) for TR haplotype analysis, which takes TR haplotype output from existing tools to perform allele size conversion, sequence comparison of haplotypes, figure plotting, comparison for allele distribution, and interactive visualization. An exemplary application of USAT for analysis of the CODIS core STR loci for DNA forensics with benchmarking human individuals demonstrated the capabilities of USAT. USAT has user-friendly graphic interfaces and runs fast in major computing operating systems with parallel computing enabled.
CONCLUSION
CONCLUSIONS
USAT is a user-friendly bioinformatics software for interpretation, visualization, and comparisons of TRs.
Identifiants
pubmed: 36402991
doi: 10.1186/s12859-022-05021-1
pii: 10.1186/s12859-022-05021-1
pmc: PMC9675219
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
497Subventions
Organisme : Office of Justice Programs
ID : 15PNIJ-21-GG-04159-RESS
Informations de copyright
© 2022. The Author(s).
Références
Bioinformatics. 2018 Jul 15;34(14):2490-2492
pubmed: 29506019
Am J Hum Genet. 2017 Nov 2;101(5):700-715
pubmed: 29100084
Nat Biotechnol. 2019 Dec;37(12):1478-1481
pubmed: 31740840
Genome Biol. 2021 Aug 13;22(1):224
pubmed: 34389037
Nucleic Acids Res. 1999 Jan 15;27(2):573-80
pubmed: 9862982
Forensic Sci Int Genet. 2018 May;34:162-169
pubmed: 29486434
Genomics Proteomics Bioinformatics. 2007 Feb;5(1):7-14
pubmed: 17572359
Bioinformatics. 2019 Mar 15;35(6):914-922
pubmed: 30165507
Nat Rev Genet. 2015 Nov;16(11):627-40
pubmed: 26442640
Nat Commun. 2021 Apr 6;12(1):2075
pubmed: 33824302
Int J Legal Med. 2021 Nov;135(6):2235-2246
pubmed: 34436655
Proc Natl Acad Sci U S A. 2019 Jul 23;116(30):15122-15127
pubmed: 31285335
Gene. 1988 Dec 15;73(1):237-44
pubmed: 3243435
Nat Methods. 2022 Jun;19(6):635-638
pubmed: 35689027
Forensic Sci Int Genet. 2021 May;52:102463
pubmed: 33493821
Cell. 2022 Sep 1;185(18):3426-3440.e19
pubmed: 36055201
Science. 2022 Apr;376(6588):44-53
pubmed: 35357919
DNA Repair (Amst). 2018 Mar;63:10-15
pubmed: 29414049
Curr Protoc Mol Biol. 2018 Apr;122(1):e59
pubmed: 29851291
Front Plant Sci. 2016 Sep 13;7:1350
pubmed: 27679641
Bioinformatics. 2021 May 5;37(5):731-733
pubmed: 32805020
Electrophoresis. 2018 Nov;39(21):2655-2668
pubmed: 29750373
N Engl J Med. 2019 Jul 4;381(1):64-74
pubmed: 31269367
Forensic Sci Int Genet. 2017 Sep;30:18-23
pubmed: 28605651
Genome Med. 2022 Aug 11;14(1):84
pubmed: 35948990
Nat Commun. 2018 Oct 23;9(1):4397
pubmed: 30353011
Science. 2022 Apr;376(6588):eabj6965
pubmed: 35357917
Front Cell Dev Biol. 2020 Jan 21;7:328
pubmed: 32076600
Brief Bioinform. 2013 Jan;14(1):67-81
pubmed: 22648964
J Mol Neurosci. 2021 Dec;71(12):2441-2455
pubmed: 34056692
Nat Methods. 2017 Jun;14(6):590-592
pubmed: 28436466
Forensic Sci Int Genet. 2017 Mar;27:27-40
pubmed: 27914278
Nucleic Acids Res. 2017 Sep 6;45(15):e142
pubmed: 28666376
Nat Rev Genet. 2009 Apr;10(4):241-51
pubmed: 19293820
Curr Opin Genet Dev. 2017 Jun;44:9-16
pubmed: 28213161