Youtor
Submitting DNA Sequences to GenBank with the help of iTaxoTools
>> YOUR LINK HERE: ___ http://youtube.com/watch?v=AYVtvK1RZJk
In this tutorial, we guide you through the process of submitting single-locus sequences, like DNA barcode FASTA alignments, to GenBank (using the NCBI submission portal or BankIt). Learn how DNAconvert, a tool from the iTaxoTools project, can streamline this process. Submitting DNA sequences and associated metadata (e.g. specimen voucher, isolate, country, coordinates, source modifiers, or reading frames) to GenBank, or other databases like the DNA Data Bank of Japan or the European Nucleotide Archive, is crucial for research publication and future accessibility under the FAIR principle. • ▬ Links Ressources ▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬ • ► Download iTaxoTools • https://itaxotools.org/download.html • ► GenBank • https://www.ncbi.nlm.nih.gov/genbank/ • ► GenBank - Source Modifiers • https://www.ncbi.nlm.nih.gov/WebSub/h... • ► BioCollections • https://www.ncbi.nlm.nih.gov/biocolle... • ► Modifiers for FASTA Definition Lines • https://www.ncbi.nlm.nih.gov/genbank/... • ► Preparing a Source Modifiers Table File • https://www.ncbi.nlm.nih.gov/WebSub/h... • ► INSDC Geographic Location List • https://www.ncbi.nlm.nih.gov/genbank/... • ► International Nucleotide Sequence Database Collaboration • https://www.insdc.org/ • ▬ References ▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬ • ► Vences, M., Miralles, A., Brouillet, S., Ducasse, J., Fedosov, A., Kharchev, V., Kostadinov, I., Kumari, S., Patmanidis, S., Scherz, M.D., Puillandre, N. Renner, S.S. (2021). iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists. Megataxa 6: 77–92. https://doi.org/10.1101/2021.03.26.43... • ► Renner, S.S., M.D. Scherz, C.L. Schoch, M. Gottschling M. Vences (2023): DNA sequences from type specimens and type strains - how to increase their number and improve their annotation in NCBI GenBank and related databases. – Systematic Biology, doi: 10.1093/sysbio/syad068. • ► Miralles, A., Bruy, T., Wolcott, K., Scherz, M. D., Begerow, D., Beszteri, B., ... Vences, M. (2020). Repositories for taxonomic data: where we are and what is missing. Systematic biology, 69(6), 1231-1253. https://doi.org/10.1093/sysbio/syaa026 • ▬ Voiceover ▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬ • ► text-to-speech AI tool offered by https://elevenlabs.io • ▬ Music ▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬ • ► Music track: Storm by Aylex • ► Source: https://freetouse.com/music • ▬ Websites ▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬ • ► TAXON-OMICS - New approaches to discovering and naming biodiversity • https://www.taxon-omics.com/ • ► iTaxoTools: https://itaxotools.org/ • ▬ Social Media ▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬ • ► Facebook: / dfg.taxonomics • ► X: / spp_taxonomics • ▬ Chapters ▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬▬ • 00:00 Introduction • 02:23 Initial preparation of the dataset • 07:44 Using the NCBI Submission Portal for standard markers • 11:01 Using BankIt to submit sequences of other markers • 14:56 Credits
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