Sequence Submission Tools

Sequence Submission Tools

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  SEQUENCE SUBMISSION TOOLS Name : RishikaMaji Course: BSc.(H) Zoology Roll no: 18/154
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  Introduction What are Sequencesubmission 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.
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  Introduction Types of SequenceSubmission Tools BankIt Sequin Webin tblast2n
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  BankIt Web-based Sequence Submission Tool Toolfor submission to NCBI GenBank Step by step submission tool for simple data Key Features:-
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  BankIt A single sequence. Afew unrelated sequences or a few sequences with different features and/or source information. A large set of sequences with a small number of the same features/source information. A small batch of sequences with a small number of features or source information. 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.
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  BankIt Website: Imageshowing the types of sequences that can be submitted through BankIt. Source : https://www.ncbi.nlm.nih.gov/WebSub/
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  BankIt BankIt can onlybe 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/ 3rd 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
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  Sequin Stand alone Sequence SubmissionTool Tool designed by NCBI Submission tool for complex biological sequences Key Features:-
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  Sequin Submitting, editing andupdating 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
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  1. The Firstpage 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
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  4. Entry ofsequence in selected format 5. Annotate the sequence to be submitted. Image Source : https://web.mit.edu/seven/src/ncbi/doc/sequin.htm
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  Preview of GenBankFlat file format Preview of Graphical view of the sequence being submitted. Image Source : https://web.mit.edu/seven/src/ncbi/doc/sequin.htm
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  Webin Tool for submissionto EMBL Submission tool for complex biological data Key Features:- Web-based Sequence Submission Tool
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  Webin This submission tooloffers 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
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  Conclusion BankIt Stand Alone software Toolby 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.