IMGT/LIGM-DB Feature Table Definition Document

Version 15, July 2004

CONTENTS

1. INTRODUCTION
2. FORMAT EXAMPLE
3. FEATURE KEYS
4. FEATURE LOCATION
5. FEATURE QUALIFIERS

1. INTRODUCTION

The feature table contains information about genes and gene products, as well as regions of biological significance reported in a sequence. It contains information on regions of the sequence that code for proteins and RNA molecules. It also enumerates differences between different reports of the same sequence and provides cross-references to other data collections, as described in more detail below.

The first two lines of the feature table in IMGT/LIGM-DB entries are feature header (FH) lines, specific to the EMBL flatfile format. The first one includes the column headers 'Key' and 'Location/Qualifier'. The second one is an empty spacer line.

Each feature consists of a feature key and a location (see below for details). If the location does not fit on the same line as the key, a continuation line may follow. If further information about the sequence is required, one or more additional lines containing feature qualifiers may follow.

Features appear on FT lines. The linetype code FT appears in columns 1-2 and columns 3-5 are blank. The feature key begins in column 6 and may be no more than 15 characters in length. The location begins in column 26. Feature qualifiers begin on subsequent FT lines at column 26. Location, qualifier, and continuation lines may extend from column 26 to 80. Each qualifier is added on a new line.

2. FORMAT EXAMPLE

An example of the feature table format is:

----+----+----+----+----+----+----+----+----+----+----+----+----+----+
        10        20        30        40        50        60        70
     Key                 Location/Qualifiers
  
     L-PART1             1..28
     V-GENE              1..222
                         /cell_type="B cell"
                         /note="NCBI gi: 483900"
                         /partial
                         /product="immunoglobulin kappa chain, V-region
                         (SPK.4)"
                         /tissue_type="Graves' thyroid"
              
----+----+----+----+----+----+----+----+----+----+----+----+----+----+
        10        20        30        40        50        60        70

Thus, there are 4 types of feature table lines:

      Line type            Content                 #/entry     #/feature
      ---------            -------                 -------     ---------

      Header               Column titles           1           N/A
      Feature descriptor   Key and location        1 to many   1
      Feature qualifiers   Qualifiers and values   N/A         0 to many
      Continuation lines   Feature descriptor or   0 to many   0 to many
                           qualifier continuation


The position of the data items within the feature descriptor line is as
follows:

     column position    data item
     ---------------    ---------

     1-5                blank (may be used to improve readability, ie FT) 
     6-24               feature key
     25                 blank
     26-80              location

Data on the qualifier and continuation lines begins in column position 26 (the first 25 columns contain blanks the first character is a '/' followed by the the qualifier discription). Qualifiers used here are the same as the EMBL qualifiers except for one exception the AA_number qualifier.

The sections below provide a brief introduction to the new feature table format.

3. FEATURE KEYS

The first item on an FT line is the feature key. It starts in column 6 and can continue to column 24. The list of valid feature keys is shown below:

4. FEATURE LOCATION

The second item on the FT line designates the location of the feature in the sequence. The location begins at column 26. Several conventions are used to indicate sequence location.

Base numbers in locations refer to the numbering in the entry, which is not necessarily the same as the numbering scheme used in the original report. The first base in the presented sequence is numbered base 1. Sequences are presented in the 5' to 3' direction.

A location can be one of the following:

      o  A single base.

      o  A contiguous span of bases.

A contiguous span of bases is indicated by the number of the first and last bases in the range separated by two periods (e.g., 23..79). Starting and ending positions can be indicated by base number.

5. FEATURE QUALIFIERS

Qualifiers provide additional information about features. They take the form of a slash (/) followed by a qualifier name and, if applicable, an equal sign (=) and a qualifier value. Feature qualifiers begin at column 26.

Qualifiers convey many types of information.  Their values can, therefore, take
several forms:

      o  Free text.

      o  Controlled vocabulary or enumerated values.

      o  Citations or reference numbers.

      o  Sequences.

      o  Feature labels.

Text qualifier values are enclosed in double quotation marks. The text can consist of any printable characters (ASCII values 32-126 decimal). If the text string includes double quotation marks, each double quotation mark must be escaped by placing a double quotation mark in front of it (e.g., /note="This is an example of ""escaped"" quotation marks").

Citation or reference numbers for an entry are enclosed in square brackets ([]) to distinguish them from other numbers.

A literal sequence of bases (e.g., "atgcatt") is enclosed in quotation marks. Literal sequences are distinguished from free text by context. Qualifiers that take free text as their values do not take literal sequences, and vice versa.

The '/label=' qualifier takes a feature label as its qualifier. Although feature labels are optional, they allow unambiguous references to features. The feature label identifies a feature within an entry; when combined with the accession number and the name of the data bank from which it came, it is a unique tag for that feature.

The following is a list of valid feature qualifiers:

This manual and the database it accompanies may be copied and redistributed freely, without advance permission, provided that this statement is reproduced with each copy. 

Last modified: July 2004

For any other use please contact Marie-Paule Lefranc lefranc@ligm.igh.cnrs.fr.