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Structures Menu

The Gap database consists of numerous records, each of one of several predefined types. The types correspond to the commands available within the Structures menu. All of these, except for the "Database" command, insert a dialogue between the menubar and whatever is underneath it. In the picture below we have selected "Annotations" from the menu which has prompted us for "Which annotation (1-105)" (the 1-105 is the valid range of inputs available).

[picture]

In the panel beneath the "Which annotation" question is a panel detailing another annotation structure. In general the structure type and number are shown at the top of the panel (in this case annotation number 100). Beneath this are the structure fields on the left followed by the values for these fields on the right. Sometimes Gap may store a value as numeric, but display the structure as both a numeric and a string describing this value. For instance here the annotation strand is "0" which is Gap's way of storing "forward".

Some values have an arrow next to them, such as with the "next" field in the illustration. Clicking on this arrow will display the structure referenced by this value. Here it is another annotation (annotation 1014). We are also told that the annotation is part of Contig number 4. Clicking on the arrow next to this will take us to that contig structure.

Selected notes on editing the structures follows.

Database Structure

There is only a single database structure, so this option does not produce any dialogue prompted for the item number. The description of the more important fields follow.

num_contigs
The number of currently used contigs

num_readings
The number of currently used readings

Ncontigs
The number of currently allocated contigs

Nreadings
The number of currently allocated readings

contigs
readings
annotations
templates
clones
vectors
notes
Record numbers of arrays holding the record numbers of each item

free_annotations
A linked list of unused annotations
free_notes
A linked list of unused notes

Reading Structure

Some reading structure fields reference the record number in the Gap database of a string. Where this string is short, such as the reading name, both the record number and the contents of the string can be edited. To edit a single name the string should be changed. To swap two reading names around either edit both strings or swap the two name record numbers.

The annotations value references an annotation number. If this is zero then this reading has no annotations.

The length is the complete length of sequence, including hidden data. The sequence_length is the length of only the used sequence. The location of the hidden data is specified by the start and end values. Note that sequence_length=end-start-1.

A left or right value of zero means that this reading has no left or right neighbour.

Contig Structure

A contig is a list of readings. The left and right values specify the first and last reading numbers in the doubly linked list representing this contig.

Annotation Structure

Annotations are stored as linked lists. Each reading and each contig has a (possibly blank) list. All other unused annotations are held on the free list. The next value is used to reference the next annotation number. A value of zero represents the end of the list.

Template Structure

The template name field can be edited as both a string and the record number pointing to that string. The template structure display has links to a vector number and a clone.

Original Clone Structure

The original clone name is often the name of the database. The use of original clones is primarily for large scale sequencing. When breaking down a sequence into cosmids and then into sequencing templates, we say that each cosmid is a clone.

Note Structure

A note may be considered as a positonless annotation (without the position, length or strand fields). Notes store both their creation and last-modification dates. Notes may be attached, in a linked-list fashion, to readings, contigs, or the database structure.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_150.html