Recent determination of human and mouse draft genome sequences should be the landmarks for the post-sequencing era. One of the major challenges in this era is the interpretation of the promoter regions. To this end, precise identification of the transcriptional start sites (TSSs) is essential. However, such an information cannot be obtained from usual cDNA or EST data. Although Eukaryotic Promo...

Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data ...

We introduce a non-parametric representation of transcription factor binding sites which can model arbitrary dependencies between positions. As two parameters are varied, this representation smoothly interpolates between the empirical distribution of binding sites and the standard position-specific scoring matrix (PSSM). In a test of generalization to unseen binding sites using 10-fold cross-va...

The sites of insertion of the transposable kanamycin-neomycin resistance-determining element, Tn5, in the E. coli K-12 chromosome were assessed in a collection of over 300 auxotrophs. Although mutations in at least 45 different cistrons were obtained, the distribution of insertion sites was not completely random: proA or proB; cysG; and cysH, cysD or cysC mutants were found in excess.

Public reporting burden for the collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including s...

One of the first events taking place when a crystal of a metalloprotein is exposed to X-ray radiation is photoreduction of the metal centres. The oxidation state of a metal cannot always be determined from routine X-ray diffraction experiments alone, but it may have a crucial impact on the metal's environment and on the analysis of the structural data when considering the functional mechanism o...

This study assessed short-range spatial heterogeneity of TNT concentrations in surface soils at explosives-contaminated sites. Discrete and composite samples were analyzed by both on-site calorimetric techniques and standard laboratory protocols. Three locations were sampled at each of three installations, and the results were used to estimate the relative contributions of analytical error and ...

Models of transcription factor (TF) binding sites provide a basis for a wide spectrum of studies in regulatory genomics, from reconstruction of regulatory networks to functional annotation of transcripts and sequence variants. While TFs may recognize different sequence patterns in different conditions, it is pragmatic to have a single generic model for each particular TF as a baseline for pract...