Function

Description

seqxref retrieves all database cross-references for a sequence entry. A list of hyperlinks to cross-referenced data is written to the screen and to file.

Usage

Command line arguments

Input file format

Output file format

The output file (that is written to screen) consists of a simple list of hyperlinks to cross-referenced data.

Data files

The EMBOSS database information file (db.dat) must be installed in the EMBOSS data directory and indexed. This is done automatically for typical installations.

Notes

Cross-references from a sequence entry to other resources are either "explicit" or "implicit" and are typically made from the database cross-reference (DR) line:

• "Explicit" links are generally of the form "DR database_name; primary_id; secondary_id". primary_id is usually an accession and secondary_id usually complements the first, e.g. entry name or version number.
• "Implicit" links are to databases that (typically) lack their own accession number scheme, but may be cross-referenced by 1) SP primary accession number or 2) some other identifier used by SP, e.g. gene name in the GN line. In both cases no extra DR line is present.

The links include:

• Cross-reference from SP via URL address under the CC topic "DATABASE" (the links are to databases that (typically) are accessed via one URL, not by individual accessions)
• Cross-reference from SP via key types in the feature table (these links are provided where the link concerns a feature)
• Cross-reference from SP to MedLine/PubMed stored in RX (Reference cross-reference) line (the RX line provides the Medline or PubMed identifier)
• Cross-reference from EMBL DR line
• Other (these include e.g. taxonomy identifier (Tax_id) that uniquely identifies an organism in NCBI taxonomy classification, and Enzyme EC numbers which are found in SP description (DE) lines.

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

Author(s)

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History

Target users

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