What is location?

Location is a mandatory field associated with a feature. It conveys information about the part of the sequence to which a feature corresponds.

Types of locations

  • simple point
    • allowed in ST.25: in the form n..n
    • translatable in the case of CDS: only in join
    • points to a single base in the presented sequence
      example: 340
  • sequence span
    • allowed in ST.25: yes
    • translatable in the case of CDS: yes, if longer then ten bases
    • The most widely used feature location is a sequence span. It is defined by the start and end point. Points to a continuous range of bases bounded by and including the start and end bases.
      Example: 340..565
  • simple left partial region
    • allowed in ST.25: no
    • translatable in the case of CDS: no
    • Indicates that the exact lower boundary point of a feature is unknown. The location begins at some base previous to the first base specified (which need not be contained in the presented sequence) and continues to and includes the end base.
      Example: 340<..565
  • simple right partial region
    • allowed in ST.25: no
    • translatable in the case of CDS: no
    • The feature starts at the first sequenced base and continues beyond the base indicated.
      Example: 1..>565
  • between location
    • allowed in ST.25: no
    • translatable in the case of CDS: no
    • Indicates that the exact location is unknown but that it is one of the bases between 102 and 110, inclusive.
      Example: 102.110
  • site
    • allowed in ST.25: no
    • translatable in the case of CDS: no
    • points to a site between bases 123 and 124.
      Example: 123^124
  • join
    • allowed in ST.25: no
    • translatable in the case of CDS: yes
    • Regions should be joined to form one contiguous sequence. The joined regions must be continuous. Only points, complements and regions are allowed.
      Example: join(12..78,134..202)
  • complement
    • allowed in ST.25: yes, if complemented location is
    • translatable in the case of CDS: no
    • Find the complement of the presented sequence in the span specified by location (i.e. read the complement of the presented strand in its 5'-to-3' direction).
      Example: complement(34..126)

The availability of a certain location type is dependent on other conditions being met: length&gt;10, length divisible by 3.

Allowed location types in BiSSAP

The location of one complex type cannot be nested in the same type. If the application contains join, it may be used on only one level. For example:
join(complement(join(x..y, ...), ...) is not allowed.

Joined locations in ST.25

“Join location” presents a special situation in ST.25. This format does not provide for join location. However, in practice, applicants extend ST.25 in the following way:

  • Write join locations in ST.25 as if they were allowed. This is against the standard description, but patent offices usually accept such files.
  • Treat all CDSs of a sequence as a join. This is a PatentIn approach. The drawback is that it is very confusing. BiSSAP can handle this situation.

Both practices are discouraged. However, if it is necessary, we recommend using the normal join, as described in the documentation linked below. Such practices will not be allowable when the proposed new XML format is applied.

BiSSAP produces output using the join operator.

More information