2.1 GenBank (Sequence Annotation Format)

Prerequisite Terminologies Before proceeding to the topic, it is important to be aware of the followings to have the better understanding:

• Accession Number
• Sequence Retrieval using NCBI
• Flat File format

GenBank GenBank format is a flat file format (also referred as GenBank Flat File Format) that organizes and stores the sequence and its annotation together. It is divided into two sections:

1. Annotation or Feature section
2. Sequence section The purpose of this highly organized way of providing additional data is to make it possible for this information to be standardized for human interpretation, and to be handled by many different computer programs.

Annotation or Feature Section The first or annotation section contains the entry’s LOCUS, DEFINITION, ACCESSION and VERSION and denoted by ORIGIN. The final detail is the actual sequence. These five elements are the essential parts of the GenBank format. The non-essential parts of the entry contain what is commonly known as metadata, and can include more detailed information about the organism, cross-references to other databases, and even a list of publications in which this entry is featured in. The FEATURES part of the entry describes important characteristics of the entry’s sequence such as presence of coding sequences, proteins, etc. The rest of this part is intended for the computer program to read it.

Sequence Section This section contains the actual sequence that we want to study. The sequence might be in the form of nucleotides or amino acids just as the FASTA format. The sequence is distributed in 6 columns and each column consists of 10 residues either nucleotides or amino acids which tells us that each row has 60 residues. At the end of the sequence ‘//’ in order to indicate the end of the entry.

Syntax The syntax for the GenBank is designed as:

LOCUS         AB000000      000 bp    mRNA    linear    PRI 01.01.1970
DEFINITION    Homo sapiens mRNA................................
ACCESSION     AB000000
ORIGIN    1 acaagatgcc attgtccccc ggcctcctgc tgctgctgct ctccggggcc acggccaccg
         61 ctgccctgcc cctggagggt ggccccaccg gccgagacag cgagcatatg caggaagcgg
        121 caggaataag gaaaagcagc ctcctgactt tcctcgcttg gtggtttgag tggacctccc
        181 aggccagtgc cgggcccctc ataggagagg aagctcggga ggtggccagg cggcaggaag
        241 gcgcaccccc ccagcaatcc gcgcgccggg acagaatgcc ctgcaggaac ttcttctgga
        301 agaccttctc ctcctgcaaa taaaacctca cccatgaatg ctcacgcaag tttaattaca
        361 gacctgaa
//

LOCUS The LOCUS field contains a number of different data elements, including locus name, sequence length, molecule type, GenBank division, and modification date.

DEFINITION Brief description of sequence; includes information such as source organism, gene name/protein name, or some description of the sequence’s function.

ACCESSION The unique identifier for a sequence record. The above example briefly describes the syntax. Originally, the GenBank format contains the huge amount of information about the sequence.

Summary In this tutorial, we’ve learnt about the GenBank format which stores the sequence as well as annotates it. And it has two sections that consists Annotation or feature section and Sequence section. We have taken the example of Homo sapiens Lactase. You can choose the sequence that you may require.

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