Sequence Submission Tools

In this presentation, I talk about the various tools for the submission of DNA or RNA sequences into various sequence databases. The sequence submission tools talked about in this presentation are BankIt, Sequin and Webin.

1. SEQUENCE SUBMISSION TOOLS Name : Rishika Maji Course: BSc.(H) Zoology Roll no: 18/154

2. Introduction What are Sequence submission tools? Submission Tools are either web-based or stand alone software which aids in submission of new biological data or updating the already existing sequence data in the various biological databases available. Sequence data is shared between several Databases on a regular basis. Each sequence or a new data is provided with an accession number after submission into a particular database which is the same for all databases.

3. Introduction

4. BankIt Web-based Sequence Submission Tool Tool for submission to NCBI GenBank Step by step submission tool for simple data Key Features:-

5. BankIt Used to submit data to GenBank of :- Source : https://www.ncbi.nlm.nih.gov/books/NBK63590/ This is used for submission of genomic DNA (protein coding genes), transcripts (e.g. mRNA, ncRNA), or small genomes (organelle, plasmid, and phage) from any organism.

6. BankIt Website: Image showing the types of sequences that can be submitted through BankIt. Source : https://www.ncbi.nlm.nih.gov/WebSub/

7. BankIt BankIt can only be used to submit simple types of biological data. It can only be used when the data does not involve any complicated annotations. It cannot be used when advanced sequence analysis tools are required . The following categories of information are necessary for sequence submission :- Reference Information- Author’s name, publication. Source information- organism genus species, taxonomic lineage, uncultured/cultured. Source category- Original sequence/ 3 rd party sequence. Features - exon, intron, CDS Sequence in FASTA format and of at least 200 nucleotides. Source : https://www.ncbi.nlm.nih.gov/WebSub/html/requirements.html

8. Sequin Stand alone Sequence Submission Tool Tool designed by NCBI Submission tool for complex biological sequences Key Features:-

9. Sequin Submitting, editing and updating both nucleotide and protein sequence data to NCBI, EMBL and DDBJ. Sequin has the capacity to handle long sequences and sets of sequences like :- segmented entries, multiple annotations, population, phylogenetic, and mutation studies . Sequin is a more sophisticated software and has advanced features like :- Graphical viewing, Automatic annotations of complex sequences, Built-in validation functions for enhanced quality assurance and better editing features. Is used for :- Source : https://web.mit.edu/seven/src/ncbi/doc/sequin.htm

10. 1. The First page of Sequin 2. Fill in the Author details. 3. Select the Sequence type and Sequence Format Image Source : https://web.mit.edu/seven/src/ncbi/doc/sequin.htm

11. 4. Entry of sequence in selected format 5. Annotate the sequence to be submitted. Image Source : https://web.mit.edu/seven/src/ncbi/doc/sequin.htm

12. Preview of GenBank Flat file format Preview of Graphical view of the sequence being submitted. Image Source : https://web.mit.edu/seven/src/ncbi/doc/sequin.htm

13. Webin Tool for submission to EMBL Submission tool for complex biological data Key Features:- Web-based Sequence Submission Tool

14. Webin This submission tool offers submission of single sequences and complex sequences in bulk. This is used when rapid submission of sequences are required. Webin is also an advanced software and can be used for multiple annotations and phylogenetic studies. SAR Webin is used for small scale submitters . Source : https://medias01-web.embl.de/Mediasite/Play/ecd0a40578b246c69c0a5b60373b8fde1d

15. Conclusion BankIt Stand Alone software Tool by NCBI Supports submission of simple and complex biological sequences. Capacity of multiple annotation and is more advanced. Is used for segmented sequences, phylogenetic and population studies and graphical view. Sequin Webin Web Based tool Tool by NCBI – GenBank Simple nucleotide sequence submission. Capacity of only simple annotations. Cannot be used for phylogenetic/population studies. Web Based tool Tool by EMBL Supports rapid submission of Complex set of sequences. Capacity of complex and multiple annotation. Advanced software used for phylogenetic and population studies.

16. Thank you!