Gap (bioinformatics)

A Gap ( engl. , In German: gap ) referred to in the bioinformatics , a gap or space in a sequence, in particular in sequence alignment . A gap means that there is another element at the corresponding point in a related sequence.

It is usually not known which sequence is evolutionarily older, i.e. by which type of mutation the sequence was changed. In the case of an insertion , an element would have been inserted at the point where the gap is now located; in the case of a deletion , conversely, an element would have been deleted, resulting in the gap. Because of these two possibilities, gaps are also known as indels .

Related terms are GOP ( gap opening penalty ), which denotes the cost of starting a gap, and GEP ( gap extension penalty ), which denotes the cost of widening a gap.