Biomedical subjects

T W Blackwell

Publications and source records attributed to T W Blackwell.

3 recordsLinked to original sources

PubMed2001

Conformational model for binding site recognition by the E.coli MetJ transcription factor.

MOTIVATION: Current methods for identifying sequence specific binding sites in DNA sequence using position specific weight matrices are limited in both sensitivity and specificity. Double strand DNA helix exhibits sequence dependent variations in conformation. Interactions between macromolecules result from complementarity of the two tertiary structures. We hypothesize that this conformational variation plays a role in transcription factor binding site recognition, and that the use of this structure information will improve the predictive power of transcription factor binding site models. RESULTS: Conformation models for the sequence dependence of DNA helix distortion have been developed. Using our conformational models, we defined a tertiary structure template for the met operon repressor MetJ binding site. Both naturally occurring sites and precursor binding sites identified through in vitro selection were used as the basis for template definition. The conformational model appears to recognize features of protein binding sites that are distinct from the features recognized by primary sequence based profiles. Combining the conformational model and primary sequence profile yields a hybrid model with improved discriminatory power compared with either the conformational model or sequence profile alone. Using our hybrid model, we searched the E.coli genome. We are able to identify the documented MetJ sites in the promoter regions of metA, metB, metC, metR and metF. In addition, we find several novel loci with characteristics suggesting that they are functional MetJ repressor binding sites. Novel MetJ binding sites are found upstream of the metK gene, as well as upstream of a gene, abc, a gene that encodes for a component of a multifunction transporter which may transport amino acids across the membrane. The false positive rate is significantly lower than the sequence profile method. AVAILABILITY: The programs of implementation of this algorithm are available upon request. The list of crystal structures used for compiling the mean base step parameters of DNA is available by anonymous ftp at http://stateslab.wustl.edu/pub/helix/StructureList.

Bacterial Proteins↗

PubMed2001

Probabilistic approaches to the use of higher order clone relationships in physical map assembly.

UNLABELLED: Physical map assembly is the inference of genome structure from experimental data. Map assembly depends on the integration of diverse data including sequence tagged site (STS) marker content, clone sizing, and restriction digest fingerprints (RDF). As experimentally measured data, these are uncertain and error prone. Physical map assembly from error free data is straightforward and can be accomplished in linear time in the number of clones, but the assembly of an optimal map from error prone data is an NP-hard problem. We present an alternative approach to physical map assembly that is based on a probabilistic view of the data and seeks to identify those features of the map that can be reliably inferred from the available data. With this approach, we achieve a number of goals. These include the use of multiple data sources, appropriate representation of uncertainties in the underlying data, the use of clone length information in fingerprint map assembly, and the use of higher order information in map assembly. By higher order information, we mean relationships that are not expressible in terms of neighbouring clone relationships. These include triplet and multiple clone overlaps, the uniqueness of STS position, and fingerprint marker locations. In a probabilistic view of physical mapping, we assert that all of the many possible map assemblies are equally likely a priori. Given experimental data, we can only state which assemblies are more likely than others given the experimental observations. Parameters of interest are then derived as likelihood weighted averages over map assemblies. Ideally these averages should be sums or integrals over all possible map assemblies, but computationally this is not feasible for real-world map assembly problems. Instead, sampling is used to asymptotically approach the desired parameters. Software implementing our probabilistic approach to mapping has been written. Assembly of mixed RDF and STS maps containing up to 60 clones can be accomplished on a desktop PC with run times under an hour. AVAILABILITY: http://stl.wustl.edu/software/gibbsmap/.

Cloning, Molecular↗

PubMed1999

Identity by descent genome segmentation based on single nucleotide polymorphism distributions.

In the course of our efforts to build extended regions of human genomic sequence by assembling individual BAC sequences, we have encountered several instances where a region of the genome has been sequenced independently using reagents derived from two different individuals. Comparing these sequences allows us to analyze the frequency and distribution of single nucleotide polymorphisms (SNPs) in the human genome. The observed transition/transversion frequencies are consistent with a biological origin for the sequence discrepancies, and this suggests that the data produced by large sequencing centers are accurate enough to be used as the basis for SNP analysis. The observed distribution of single nucleotide polymorphisms in the human genome is not uniform. An apparent duplication in the human genome extending over more than 130 kb between chromosomes 1p34 and 16p13 is reported. Independently derived sequences covering these regions are more than 99.9% identical, indicating that this duplication event must have occurred quite recently. FISH mapping results reported by the relevant laboratories indicate that the human population may be polymorphic for this duplication. We present a population genetic theory for the expected distribution of SNPs and derive an algorithm for probabilistically segmenting genomic sequence into regions that are identical by descent (IBD) between two individuals based on this theory and the observed locations of polymorphisms. Based on these methods and a random mating model for the human population, estimates are made for the mutation rate in the human genome.

Algorithms↗