Novel DNA sequence representations

Optimal Dynamic Sequence Representations

We describe a data structure that supports access, rank and select queries, as well as symbol insertions and deletions, on a string S[1, n] over alphabet [1..σ] in time O(lgn/ lg lgn), which is optimal. The time is worst-case for the queries and amortized for the updates. This complexity is better than the best previous ones by a Θ(1 + lg σ/ lg lgn) factor. Our structure uses nH0(S) + O(n + σ(l...

Sequence heterogeneity in kinetoplast minicircle DNA of Leishmania majer

Design of novel sequence-specific DNA-binding proteins.

The design and selection of DNA-binding proteins or individual domains capable of novel sequence recognition continues to make great strides. Recent studies have also highlighted the role of the non-DNA-contacting portions of the protein and the optimal assembly of the domains. For the first time, it appears that it is possible to produce proteins capable of targeting any gene with an 18 base p...

A new moderately repetitive DNA sequence family of novel organization.

In cloning adenovirus homologous sequences, from a human cosmid library, we identified a moderately repetitive DNA sequence family consisting of tandem arrays of 2.5 kb members. A member was sequenced and several non-adjacent, 15-20 bp G-C rich segments with homology to the left side of adenovirus were discovered. The copy number of 400 members is highly conserved among humans. Southern blots o...

Novel method for identifying sequence-specific DNA-binding proteins.

We developed a general method for the enrichment and identification of sequence-specific DNA-binding proteins. A well-characterized protein-DNA interaction is used to isolate from crude cellular extracts or fractions thereof proteins which bind to specific DNA sequences; the method is based solely on this binding property of the proteins. The DNA sequence of interest, cloned adjacent to the lac...