File {SMRUCC.genomics.Assembly.NCBI.GenBank.GBFF}

.NET clr documentation

File

Description

NCBI GenBank database file.

The National Center for Biotechnology Information (NCBI) GenBank® database is a comprehensive, annotated collection of all publicly available nucleotide sequences and their protein translations. It is a key resource for bioinformatics researchers and scientists around the world. Here is an introduction to the GenBank database file: What is GenBank? Establishment: GenBank was established in 1982 and is maintained by the NCBI, which is part of the National Library of Medicine (NLM) at the National Institutes of Health (NIH) in the United States. Content: It contains sequences from various sources, including genomic, transcriptomic, and metagenomic studies, as well as sequences from viruses, prokaryotes, eukaryotes, and organelles. Purpose: The primary purpose of GenBank is to provide scientists with a reliable and freely accessible database to deposit and retrieve genetic sequence data. Key Components of a GenBank File: A GenBank file is typically composed of several sections, each containing specific information about the sequence entry. Here are the main components: Header Section: This includes the LOCUS line, which provides a summary of the entry, including the length of the sequence, the type of molecule (DNA, RNA, or protein), the date of the last update, and the unique accession number. Definition Line: This is the DEFINITION line, which gives a brief description of the sequence. Accession and Version: The ACCESSION line contains the unique identifier for the sequence entry, and the VERSION line indicates the version number of the entry and may include a secondary accession number. Keywords: The KEYWORDS line provides terms that are associated with the sequence and can be used for searching. Source: The SOURCE section describes the organism from which the sequence was derived, including taxonomy and often the specific tissue or cell type. References: This section lists the literature citations associated with the sequence data, including the authors, title, journal, and publication year. Comment: The COMMENT section can contain various types of information, such as the method used for sequence determination, the experimental procedures, or additional notes relevant to the sequence. Features Table: This is one of the most important sections, as it provides a detailed annotation of the sequence. It includes feature key-value pairs that describe the locations and characteristics of genes, exons, introns, regulatory regions, and other sequence features. Sequence Data: The actual nucleotide sequence is presented in the sequence data section, usually in a 60-character-per-line format. This section can be quite long depending on the size of the sequence. File Format: GenBank files are typically plain text files and can be opened with any text editor. However, they are often handled using bioinformatics tools and software that can parse and interpret the data more effectively. The file extension for GenBank files is usually .gb or .gbk. How to Access GenBank: You can access GenBank directly through the NCBI website (https://www.ncbi.nlm.nih.gov/genbank/) Sequences can be searched by various criteria, including accession number, keyword, author, or organism name. Users can also download sequences in various formats, including GenBank flatfile format, FASTA, and others. GenBank providing a wealth of data that scientists use for comparative genomics, evolutionary studies, and many other types of biological research.

Declare

            
# namespace SMRUCC.genomics.Assembly.NCBI.GenBank.GBFF
export class File {
   # LocusID, GI or AccessionID
   Accession: ACCESSION;
   Comment: COMMENT;
   DbLinks: DBLINK;
   # The definition value for this organism's GenBank data.
   Definition: DEFINITION;
   Features: FEATURES;
   # 这个Genbank对象是否具有序列数据
   HasSequenceData: boolean;
   # Is plasmid source?
   isPlasmid: boolean;
   # This GenBank data is the WGS(Whole genome shotgun) type data.
   IsWGS: boolean;
   Keywords: KEYWORDS;
   # The brief entry information of this genbank data.
   Locus: LOCUS;
   # This GenBank keyword section stores the sequence data for this database.
   Origin: ORIGIN;
   Reference: REFERENCE;
   # 物种信息
   Source: SOURCE;
   # Gets the original source brief entry information of this genome.(获取这个基因组的摘要信息)
   SourceFeature: Feature;
   # 物种数据
   Taxon: string;
   Version: VERSION;
}

        

.NET clr type reference tree

1. use by property member Accession: ACCESSION
2. use by property member Comment: COMMENT
3. use by property member DbLinks: DBLINK
4. use by property member Definition: DEFINITION
5. use by property member Features: FEATURES
6. use by property member Keywords: KEYWORDS
7. use by property member Locus: LOCUS
8. use by property member Origin: ORIGIN
9. use by property member Reference: REFERENCE
10. use by property member Source: SOURCE
11. use by property member SourceFeature: Feature
12. use by property member Version: VERSION

---