Structures Menu

• Database structure
• Reading structure
• Contig structure
• Annotation structure
• Template structure
• Original clone structure
• Vector structure

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 "Template" from the menu which has prompted us for "Which template (1-89)" (the 1-89 is the valid range of inputs available).

In the illustration beneath the "Which template" question is a panel detailing the annotation structure. In general the structure type and number are shown at the top of the panel (annotation number 111). 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 "1" which is Gap's way of storing "reverse".

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 zero in fact, which is invalid and is used to terminate the linked list). 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

Record numbers of arrays holding the record numbers of each item

free_annotations

A linked list of unused annotations

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 is the doubly linked list creating 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 templates, we say that each cosmids is a clone.

Vector Structure

The vector contains the name of the sequencing or cloning vector. The "cloning vector" is that used for producing the "original clone". The level of a vector used for sequence a template is 2 and for an "original clone" it is 1.