5.2 PROSITE Field Definitions

The field codes found in a PROSITE flat file help to arrange the information for human readability and machine-based parsing. There are several PROSITE field codes found in an entry; each is represented with a two-letter abbreviation. Table 5-1 provides definitions and descriptions of these field codes.

Table 5-1. PROSITE field definitions

Field

Definition

Description

ID

Identification

The second item indicates the type of entry:

PATTERN
MATRIX
RULE

AC

Accession number

PSnnnnn.

DT

Date

Date of entry or last modification of the entry.

DE

Short description

Descriptive information about the entry content.

PA

Pattern

The definition of a PROSITE pattern.

MA

Matrix/profile

The definition of a PROSITE profile/matrix.

RU

Rule

The definition of a PROSITE rule.

NR

Numerical results

This contain information relevant to the results of the scan with a pattern on the complete SWISS-PROT knowledgebase. The following qualifiers are used:

/RELEASE
/TOTAL
/POSITIVE
/UNKNOWN
/FALSE_POS
/FALSE_NEG
/PARTIAL

CC

Comments

Various types of comments. The following qualifiers are used.

/TAXO-RANGE
/MAX-REPEAT
/SITE
/SKIP-FLAG
/MATRIX_TYPE
/SCALING_DB
/AUTHOR
/FT_KEY
/FT_DESC

DR

Cross-references to SWISS-PROT

These are used as pointers to SWISS-PROT entries.

3D

Cross-references to PDB

These are used to list the Protein Data Bank entries.

DO

Pointer to the documentation file

This contains a pointer to the entry in the PROSITE documentation file that describes the entry.

//

Termination line

This designates the end of an entry.



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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