<<–2/”>a href=”https://exam.pscnotes.com/5653-2/”>h2>The <gi> Tag: A Comprehensive Guide
What is the <gi> Tag?
The <gi> tag, short for “Generic Identifier,” is an XML element used to represent a unique identifier for a biological sequence. It is part of the GenBank and EMBL sequence databases, which are widely used repositories for storing and sharing genetic information.
Structure and Attributes of the <gi> Tag
The <gi> tag is a simple element with a single attribute:
id: This attribute holds the unique identifier for the sequence. The identifier is a numerical value that is assigned by the Database.
Example:
xml
<GBSeq>
<gi id="12345678"/>
<GBSeq_locus>NM_000014</GBSeq_locus>
<GBSeq_length>1000</GBSeq_length>
<GBSeq_strandedness>single</GBSeq_strandedness>
<GBSeq_moltype>mRNA</GBSeq_moltype>
<GBSeq_definition>Human gene X</GBSeq_definition>
<GBSeq_primary_accession>NM_000014</GBSeq_primary_accession>
<GBSeq_other_seqids>
<GBSeq_other_seqid>gi|12345678|ref|NM_000014.1|</GBSeq_other_seqid>
</GBSeq_other_seqids>
<GBSeq_source>Homo sapiens</GBSeq_source>
<GBSeq_organism>Homo sapiens</GBSeq_organism>
<GBSeq_taxonomy>Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Gnathostomata; Tetrapoda; Mammalia; Eutheria; Primates; Haplorhini; Catarrhini; Hominidae; Homo</GBSeq_taxonomy>
<GBSeq_references>
<GBReference>
<GBReference_pubmed>12345678</GBReference_pubmed>
<GBReference_title>A new gene in humans</GBReference_title>
</GBReference>
</GBSeq_references>
</GBSeq>
In this example, the <gi> tag has an id attribute with the value “12345678,” representing the unique identifier for the sequence.
Usage of the <gi> Tag
The <gi> tag is used to identify a specific sequence within the GenBank or EMBL databases. It acts as a unique key to access and retrieve information about the sequence.
Here are some common uses of the <gi> tag:
- Retrieving sequence information: The
<gi>tag can be used to retrieve the sequence data, annotation, and other information associated with a specific sequence. - Cross-referencing between databases: The
<gi>tag can be used to link sequences across different databases, such as GenBank and EMBL. - Searching for sequences: The
<gi>tag can be used to search for sequences with specific identifiers.
Importance of the <gi> Tag
The <gi> tag plays a crucial role in the management and organization of biological sequence data. It provides a standardized and unambiguous way to identify and reference sequences, facilitating data sharing and collaboration among researchers.
Frequently Asked Questions (FAQs)
1. What is the difference between a gi and an accession number?
A gi is a unique identifier assigned by GenBank or EMBL to a specific sequence. An accession number is a unique identifier assigned to a specific entry in the database, which may contain multiple sequences. A gi is always associated with a specific sequence, while an accession number can be associated with multiple sequences.
2. How can I find the gi for a specific sequence?
You can find the gi for a specific sequence by searching the GenBank or EMBL databases using the sequence’s accession number or other identifiers. You can also use online tools like the NCBI Entrez system to search for sequences by gi.
3. Can a gi be reused for different sequences?
No, a gi is a unique identifier and cannot be reused for different sequences. Each sequence in GenBank or EMBL has a unique gi.
4. What is the format of a gi?
A gi is a numerical value, typically a large integer.
5. How do I cite a sequence using its gi?
You can cite a sequence using its gi by including the gi number in the citation. For example, “The sequence with gi 12345678 was used in this study.”
6. What is the relationship between a gi and a RefSeq ID?
A RefSeq ID is a unique identifier assigned to a specific sequence in the RefSeq database, which is a curated subset of GenBank. A gi can be associated with a RefSeq ID, but not all RefSeq IDs have a corresponding gi.
7. What is the difference between a gi and a PubMed ID?
A gi is a unique identifier for a biological sequence, while a PubMed ID is a unique identifier for a scientific publication.
8. What is the future of the <gi> tag?
The <gi> tag is still widely used in the GenBank and EMBL databases. However, with the increasing use of other identifiers, such as accession numbers and RefSeq IDs, the role of the <gi> tag may evolve in the future.
Table 1: Comparison of Identifiers in Sequence Databases
| Identifier | Description | Usage |
|---|---|---|
gi |
Unique identifier for a specific sequence | Identifying and retrieving sequence information |
| Accession number | Unique identifier for a specific entry in the database | Identifying and retrieving entries in the database |
| RefSeq ID | Unique identifier for a specific sequence in the RefSeq database | Identifying and retrieving curated sequences |
| PubMed ID | Unique identifier for a scientific publication | Identifying and retrieving scientific publications |
Table 2: Examples of <gi> Tag Usage
| Example | Description |
|---|---|
<gi id="12345678"/> |
Represents the unique identifier “12345678” for a specific sequence. |
<GBSeq_other_seqids><GBSeq_other_seqid>gi|12345678|ref|NM_000014.1|</GBSeq_other_seqid></GBSeq_other_seqids> |
Shows the gi “12345678” associated with the RefSeq ID “NM_000014.1”. |
<GBReference_pubmed>12345678</GBReference_pubmed> |
Indicates that the publication with PubMed ID “12345678” is associated with the sequence. |