The global genome nucleotide excision repair factor XPC firstly detects DNA lesions and then recruits a ten-subunit complex TFIIH through binding to the subunit p62 to unwind the damaged DNA for excision repair. This data article contains detailed nuclear magnetic resonance (NMR) restraints (nuclear Overhauser enhancement (NOE)-derived distance restraints, dihedral angle restraints, and hydroge...

DNA in a human cell is approximately 2 m long but is compacted into micrometre-sized eukaryotic nuclei. To achieve this level of compaction, DNA is first wrapped up into nucleosomes, which are then thought to fold into fibres and loops. The basal unit of such folding is the 10 nm ‘beads on a string’ structure observed in all eukaryotic cells (Fig 1A; reviewed in [1]). The 10 nm fibre is subsequ...

Motivation: Approximate String Matching is a pivotal problem in the field of computer science. It serves as an integral component for many string algorithms, most notably, DNA read mapping and alignment. The improved LV algorithm proposes an improved dynamic programming strategy over the banded SmithWaterman algorithm but suffers from support of a limited selection of scoring schemes. In this p...

Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform and also supports rapid random access to the underlying data. The main difficulty of relative compression is in selecting an appropriate reference sequence. In...

This thesis considers the smallest grammar problem: find the smallest context-free grammar that generates exactly one given string. We show that this problem is intractable, and so our objective is to find approximation algorithms. This simple question is connected to many areas of research. Most importantly, there is a link to data compression; instead of storing a long string, one can store a...

We consider two elementary forms of string rewriting called guided insertion/deletion and guided rewriting. The original strings are modified depending on the match with a given set of auxiliary strings, called guides. Guided insertion/deletion considers matching of a string and a guide with respect to a specific correspondence of strings. Guided rewriting considers matching of a string and a g...

One of the most studied problems in the field of computational biology is the string matching problem. Much of the reasearch has focused on developing efficient algorithms for transforming one string into another by minimizing the number of steps. The biological motivation for this problem comes from the fact that DNA sequences get transformed by a series of basic operations such as mutations, ...

MOTIVATION Exact-match overlap graphs have been broadly used in the context of DNA assembly and the shortest super string problem where the number of strings n ranges from thousands to billions. The length ℓ of the strings is from 25 to 1000, depending on the DNA sequencing technologies. However, many DNA assemblers using overlap graphs suffer from the need for too much time and space in constr...

Eukaryotes package DNA into nucleosomes that contain a core of histone proteins. During DNA replication, nucleosomes are disrupted and re-assembled with newly synthesized histones and DNA. Despite much progress, it is still unclear why higher eukaryotes contain multiple core histone genes, how chromatin assembly is controlled, and how these processes are coordinated with cell cycle progression....