Table of Contents
Closest String and Closest Substring Problems
Here, you can find the benchmark sets used in our study of CSP and CSSP. Detailed descriptions can be found in the paper:
- M. Chimani, M. Woste, S. Böcker. A Closer Look at the Closest String and Closest Substring Problem. SIAM Workshop on Algorithm Engineering & Experiments 2011, San Francisco (ALENEX11), pp. 13-24, SIAM, 2011. (link to published version)
Instances
| Type | Description | Filename | Solutions |
|---|---|---|---|
| CSP | Random | csp_rnd.tar.bz2 (135 MB) | results_csp_rnd.csv |
| CSP | McClure 1) | mcclure.tar.bz2 (2.7 KB) | results_mcclure.csv |
| CSP | Hufsky 2) | hufsky.tar.bz2 (175 KB) | results_hufsky.csv |
| CSSP | Random | cssp_rnd.tar.bz2 (119 KB) | results_cssp_rnd.csv |
File format for CSP instances
The tar.bz2-files contain simple text files where each text file contains a single instance. The naming scheme for these files is as follows:
Random instances: |Σ|-k-n-r-i.csp McClure instances: McClure-p-|Σ|-k-n.csp Hufsky instances: Hufsky-k-n-i.csp
with
| Symbol | Description |
|---|---|
| p | page of McClure paper |
| |Σ| | size of alphabet Σ |
| k | number of strings |
| n | length of strings |
| r | distance ratio such that α=n/r |
| i | instance number (10 instances are generated for each parameter combination for random instances, 100 for Hufsky instances) |
The format of a text file is as follows:
<Alphabet-size (|Σ|)> <Number of Strings (k)> <Length of Strings (n)> <1st Character of the Alphabet Σ> ... <|Σ|-th Character of the Alphabet Σ> <1st String> ... <k-th String>
File format for CSSP instances
The tar.bz2-files contain simple text files where each text file contains a single instance. The naming scheme for these files is as follows:
{i,r}-|Σ|-k-n-l-d-{l,e}-i.cssp
with
| Symbol | Description |
|---|---|
| {i,r} | i stands for implanted motif, r represents random instances |
| |Σ| | size of alphabet Σ |
| k | number of strings |
| n | length of strings |
| l | length of target string |
| d | distance |
| {l,e} | e stands for instances with E(l,d)≈1, l stands for instances with E(l,d)≈0.01, omitted in case of random instances |
| i | instance number (5 instances are generated for each parameter combination) |
For implanted motif instances there are also files ending with .sup. These files contain supplemental information about the instances (see below).
The format of a .cssp file is as follows:
<Alphabet Size (|Σ|)> <Number of Strings (k)> <Length of Strings (n)> <Length of Target String (l)> <1st Character of the Alphabet Σ> ... <|Σ|-th Character of the Alphabet Σ> <1st String> ... <k-th String>
The format of a .sup file is as follows:
<Implanted Master Substring> <Distance (d) of the Implanted Master Substring> <Position of Implanted Master Substring in the 1st String> ... <Position of Implanted Master Substring in the k-th String>
File format for solution files
The solution files are plain text files in the CSV format with a semicolon as delimiter. The first line of a file serves as a column header. Each further line represents a specific instance. The column headers are as follows:
| Header | Description |
|---|---|
| filename | the filename of the specific instance |
| formulation | only for CSSP instances: formulation used to solve the instance where d stands for δ |
| lb | lower bound of the solution value |
| ub | upper bound of the solution value |
| time | running time in seconds |