10.1016/S0166-218X(03)00187-2
Cieliebak, Mark
Mark
Cieliebak
Erlebach, Thomas
Thomas
Erlebach
Lipták, Zsuzsanna
Zsuzsanna
Lipták
Stoye, Jens
Jens
Stoye0000-0002-4656-7155
Welzl, Emo
Emo
Welzl
Algorithmic complexity of protein identification: combinatorics of weighted strings
2004
2016-01-18T09:11:15Z
2018-07-24T12:59:15Z
journal_article
https://pub.uni-bielefeld.de/record/1773560
https://pub.uni-bielefeld.de/record/1773560.json
urn:nbn:de:0070-pub-17735609
bytes
application/pdf
We investigate a problem which arises in computational biology: Given a constant-size alphabet [Mathematical script A] with a weight function µ : [Mathematical script A] --> [Double-struck N], find an efficient data structure and query algorithm solving the following problem: For a string [sigma] over [Mathematical script A] and a weight [Mathematical italic M] [element of] [Double-struck N], decide whether [sigma] contains a substring with weight [Mathematical italic M], where the weight of a string is the sum of the weights of its letters (One-String Mass Finding Problem). If the answer is yes, then we may in addition require a witness, i.e., indices i [less-than or equal to] j such that the substring beginning at position i and ending at position j has weight [Mathematical italic M]. We allow preprocessing of the string and measure efficiency in two parameters: storage space required for the preprocessed data and running time of the query algorithm for given [Mathematical italic M]. We are interested in data structures and algorithms requiring subquadratic storage space and sublinear query time, where we measure the input size as the length n of the input string [sigma]. Among others, we present two non-trivial efficient algorithms: Lookup solves the problem with O(n) storage space and O(n/log n) time; Interval solves the problem for binary alphabets with O(n) storage space in O(log n) query time. We introduce other variants of the problem and sketch how our algorithms may be extended for these variants. Finally, we discuss combinatorial properties of weighted strings.