The field codes found in a Pfam flat file help display information for human readabilty and machine-based parsing. A typical entry contains several two-letter Pfam field codes. Table 4-1 provides definitions and descriptions of these codes.
Table 4-1. Pfam field definitions
PFxxxxx or PBxxxxxx.
15 characters or less.
80 characters or less.
Author of the entry.
Alignment method of seed
Method used to align the seed members. Approved AL lines are:
HMM building command lines
Source of seed
The source suggesting seed members belong to a family.
Search threshold to build the full alignment.
This field refers to the bit scores of the highest scoring match not in the full alignment.
This field refers to the bit scores of the lowest scoring match in the full alignment.
The type field is a compulsory field describing the type of family. At present it can be one of:
Comment for database reference.
Reference to external database.
Comment for literature reference.
Digit in square brackets.
Eight digit number.
Title of paper.
Author of paper.
Location of paper.
Comment lines provide annotation and other information.
Indicated those cases where there is a nested domain.