Question

Which one of the following is a depiction of the GenBank sequence entry format?

1. >YCZ2_YEAST protein in HMR 3′ region MKAVVIEDGKAVVKEGVPIPELEEGFVGNPTDWAHIDYKVGPQSILGCDAAGQG*

2. BASE COUNT 215 A 224 G 263 G 250 T ORIGIN Filename, Length of sequence, Date, … 1 GAATTCGATA AATCTCTGGT TTATTGTGCA 51 CTTTGCTGTA AGCATAACTG CAGGGGGCGG

3. LOCUS name of locus, length and type of sequence. classification of organism, data of entry DEFINITION description of entry KEYWORDS key words for cross referencing this entry SOURCE … ORGANISM… REFERENCE… COMMENT… FEATURES… BASE COUNT… ORIGIN text indicating start of sequence 1 GAATTCGATA AATCTCTGGT TTATTGTGCA 51 CTTTGCTGTA AGCATAACTG CAGGGGGCGG //

4. >P1; ILEC lexA repressor Escherichia coli MKALTARQQEVFDLIRDHISQTGMPPTRAE IAQRLGFRSPNAAEEHLKALARKGVIEIVS

Detailed Explanation

GenBank is a comprehensive database that contains annotated sequences of a variety of organisms. Each sequence entry follows a standard format. Let’s break down each of the options:

Option 1:

>YCZ2_YEAST protein in HMR 3′ region MKAVVIEDGKAVVKEGVPIPELEEGFVGNPTDWAHIDYKVGPQSILGCDAAGQG*

• This is a sequence description format, typically used in FASTA format, which provides the sequence identifier (e.g., YCZ2_YEAST) followed by a description of the sequence. However, this does not match the GenBank sequence entry format, which contains more detailed information about the sequence, including annotations, references, and other metadata.

Option 2:

BASE COUNT 215 A 224 G 263 G 250 T ORIGIN Filename, Length of sequence, Date, … 1 GAATTCGATA AATCTCTGGT TTATTGTGCA 51 CTTTGCTGTA AGCATAACTG CAGGGGGCGG

• This option seems to include parts of a sequence with some base counts and origin data. It appears closer to the GenBank format, but it is incomplete and lacks other important components like LOCUS, DEFINITION, SOURCE, and FEATURES.

• BASE COUNT and ORIGIN are part of the GenBank format, but this option is not complete enough to be a full GenBank entry.

Option 3:

LOCUS name of locus, length and type of sequence. classification of organism, data of entry DEFINITION description of entry KEYWORDS key words for cross referencing this entry SOURCE … ORGANISM… REFERENCE… COMMENT… FEATURES… BASE COUNT… ORIGIN text indicating start of sequence 1 GAATTCGATA AATCTCTGGT TTATTGTGCA 51 CTTTGCTGTA AGCATAACTG CAGGGGGCGG //

• This option accurately depicts the structure of a GenBank sequence entry.

  • LOCUS: Name, length, and type of sequence.

  • DEFINITION: Description of the sequence.

  • KEYWORDS: Keywords for cross-referencing.

  • SOURCE: The organism from which the sequence originates.

  • FEATURES: Details about features of the sequence.

  • BASE COUNT: The number of each base in the sequence.

  • ORIGIN: The actual nucleotide sequence data.

  The structure provided here matches the standard GenBank format, making this the correct answer.

Option 4:

>P1; ILEC lexA repressor Escherichia coli MKALTARQQEVFDLIRDHISQTGMPPTRAE IAQRLGFRSPNAAEEHLKALARKGVIEIVS

• This is another FASTA format entry, similar to Option 1. It contains the identifier (P1) and the protein sequence of lexA repressor from Escherichia coli. However, it lacks detailed metadata such as the LOCUS, DEFINITION, and FEATURES sections, making it not in the GenBank format.

Correct Answer: 3

The format provided in Option 3 corresponds to a GenBank sequence entry format. It contains detailed information such as the LOCUS, DEFINITION, FEATURES, and ORIGIN, which are key components of the GenBank entry structure.

Conclusion

The GenBank sequence entry format is an important tool for bioinformatics, providing a structured way to store and share genetic sequence data. Option 3 is the correct example, as it fully captures the comprehensive information included in a GenBank entry.