Sequence
Submission Tools (BankIt, Sequin, Webin)
There are several tools facilitate the submission of sequence data to biological databases like GenBank, EMBL, and DDBJ those tools are known as Sequence Submission Tools. The most widely-used sequence submission tools are BankIt, Sequin, and Webin. A brief description of those tools are given bellow-
1. BankIt
BankIt is a web-based sequence submission tool provided by the National Center for Biotechnology Information (NCBI) for direct submission to the GenBank database. It is designed to simplify the submission of sequence data by using an intuitive, step-by-step interface.
Features:
1) Web-based and easy-to-use, requiring no software installation.
2) Suitable for submitting single or multiple sequences of nucleotide data (DNA/RNA).
3) Guides users through the submission process by asking questions about the sequence (e.g., organism name, sequence type, source).
4) It includes built-in validation to check for format errors and inconsistencies before submission.
Applications:
1) Ideal for submitting small to medium-sized datasets such as individual gene sequences.
2) Frequently used by researchers submitting gene sequences from newly discovered organisms, viral genomes, or segments of DNA for functional studies.
Advantages:
1) User-friendly interface, accessible to researchers with limited bioinformatics experience.
2) Immediate validation checks help reduce submission errors.
2. Sequin
Sequin is a standalone sequence submission tool also provided by NCBI, primarily designed for more complex submissions to Genbank.
Features:
a. Available as downloadable software, suitable for more detailed and bulk submissions.
b. Supports submission of nucleotide sequences and associated annotations, including genomic sequences, alignments, and features like coding regions, exons, and introns.
c. Sequin can handle complex data like large-scale genome projects, including microbial, plant, or animal genomes, and multi-segmented viral sequences.
d. Allows batch submission of multiple sequences, making it useful for high-throughput projects.
Applications:
a. Suitable for larger projects that involve many sequences or complex annotations.
b. Commonly used by genome sequencing projects, research labs working on large datasets, and researchers submitting metagenomic data.
Advantages:
- Supports detailed annotations and batch submissions.
- Allows for customization and editing of sequence annotations.
3. Webin
Webin is a submission system developed by the European Nucleotide Archive (ENA) for submitting nucleotide sequence data to the EMBL-EBI database.
Features:
a. Webin provides a flexible submission process, allowing users to upload nucleotide sequences (DNA/RNA) and associated metadata.
b. Supports various submission types, including raw sequence reads, assemblies, and annotated sequences.
c. Offers both web-based and programmatic submission options (for large-scale, automated submissions).
d. Provides validation tools that check for format consistency and metadata accuracy, ensuring the quality of the submitted data.
Applications:
a. Used by researchers submitting genomic sequences, including next-generation sequencing (NGS) reads, assemblies, and other annotated sequences to EMBL.
b. Popular for high-throughput sequencing projects and submissions requiring complex annotations.
Advantages:
a. Programmatic submission allows large data upload from sequencing facilities.
b. ENA's interface integrates with other EMBL-EBI services for further data analysis.
