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PubMed1995

A frameshift error detection algorithm for DNA sequencing projects.

During the determination of DNA sequences, frameshift errors are not the most frequent but they are the most bothersome as they corrupt the amino acid sequence over several residues. Detection of such errors by sequence alignment is only possible when related sequences are found in the databases. To avoid this limitation, we have developed a new tool based on the distribution of non-overlapping 3-tuples or 6-tuples in the three frames of an ORF. The method relies upon the result of a correspondence analysis. It has been extensively tested on Bacillus subtilis and Saccharomyces cerevisiae sequences and has also been examined with human sequences. The results indicate that it can detect frameshift errors affecting as few as 20 bp with a low rate of false positives (no more than 1.0/1000 bp scanned). The proposed algorithm can be used to scan a large collection of data, but it is mainly intended for laboratory practice as a tool for checking the quality of the sequences produced during a sequencing project.

Algorithms↗

PubMed2004

Effective blood signal suppression using double inversion-recovery and slice reordering for multislice fast spin-echo MRI and its application in simultaneous proton density and T2 weighted imaging.

PURPOSE: To design a multislice double inversion-recovery fast spin-echo (FSE) sequence, with k-space reordered by inversion time at slice position (KRISP) technique, to produce black-blood vessel wall magnetic resonance imaging (MRI). MATERIALS AND METHODS: In this sequence, central k-space sampling for each slice is required at inversion time (TI) of the blood signal. To fill the entire k-space, the peripheral lines are obtained less or greater the TI and using a rotating slice order. Blood flow signal suppression was first evaluated using a phantom. Simulation studies were used to investigate FSE image quality. The final sequence was then applied to the rabbit abdominal aorta MRI at 4.7 T. RESULTS: In the flow phantom study, artifacts from slow-flowing water were substantially reduced by the KRISP technique; residual water spins were dephased by the strong phase-encoding gradient required for peripheral k-space. These dephased spins flowed into the slice plane where the center of k-space was being acquired at the TI of the flowing water signal. Multislice black-blood MR images were successfully obtained in the rabbit abdomen using the sequence with the k-trajectory optimized by the simulation study. CONCLUSION: The KRISP technique was effective both in multislice double inversion-recovery FSE and in blood signal suppression.

Abdomen↗

PubMed2002

Sequencing by hybridization (SBH): advantages, achievements, and opportunities.

Efficient DNA sequencing of the genomes of individual species and organisms is a critical task for the advancement of biological sciences, medicine and agriculture. Advances in modern sequencing methods are needed to meet the challenge of sequencing such megabase to gigabase quantities of DNA. Two possible strategies for DNA sequencing exist: direct methods, in which each base position in the DNA chain is determined individually (e.g., gel sequencing or pyrosequencing), and indirect methods, in which the DNA sequence is assembled based on experimental determination of oligonucleotide content of the DNA chain. One promising indirect method is sequencing by hybridization (SBH), in which sets of oligonucleotides are hybridized under conditions that allow detection of complementary sequences in the target nucleic acid. The unprecedented sequence search parallelism of the SBH method has allowed development of high-throughput, low-cost, miniaturized sequencing processes on arrays of DNA samples or probes. Newly developed SBH methods use DNA ligation to combine relatively small sets of short probes to score potentially tens of millions of longer oligonucleotide sequences in a target DNA. Such combinatorial approaches allow analysis of DNA samples of up to several kilobases (several times longer than allowed by current direct methods) for a variety of DNA sequence analysis applications, including de novo sequencing, resequencing, mutation/SNP discovery and genotyping, and expression monitoring. Future advances in biochemistry and implementation of detection methods that allow single-molecule sensitivity may provide the necessary miniaturization, specificity, and multiplexing efficiency to allow routine whole genome analysis in a single solution-based hybridization experiment.

Base Sequence↗

PubMed2003

Radiotherapy treatment planning of prostate cancer using magnetic resonance imaging alone.

PURPOSE: Accurate anatomical delineation of the gross tumour volume (GTV) is crucial for effective radiotherapy (RT) treatment of prostate cancers. Although reference to pelvic magnetic resonance (MR) for improved delineation of the prostate is a regular practice in some clinics, MR has not replaced CT due to its geometrical distortions and lack of electron-density information. The possibility and practicality of using MR only for RT treatment planning were studied. MATERIALS AND METHODS: The addition of electron-density information to MR images for conformal radiotherapy (CRT) planning of the prostate was quantified by comparing dose distributions created on the homogeneous density- and bulk-density assigned images to original CT for four patients. To quantify the MR geometrical distortions measurements of a phantom imaged in CT (Siemens Somatom Plus 4) and FLASH 3D T1-weighted MR (1.5 T whole body Siemens Magnetom Vision) were compared. Dose statistics from CRT treatment plans made on CT and MR for five patient data were compared to determine if MR-only treatment plans can be made. RESULTS: The differences between dose-plans on bulk-density assigned images when compared to CT were less than 2% when water and bone values were assigned. Dose differences greater than 2% were observed when images of homogeneous-density assignment were compared to the CT. Phantom measurements showed that the distortions in the FLASH 3D T1-weighted MR averaged 2 mm in the volume of interest for prostate RT planning. For the CT and MR prostate planning study, doses delivered to the planning target volume (PTV) in CT and MR were always inside a 93-107% dose range normalised to the isocentre. Also, the doses to the organs-at-risk in the MR images were similar to the doses delivered to the volumes in the registered CT image when the organ volumes between the two images were similar. CONCLUSIONS: Negligible differences were observed in dose distribution between CRT plans using bone+water CT number bulk-assigned image and original CT. Also, the MR distortions were reduced to negligible amounts using large bandwidth MR sequence for prostate CRT planning. MR treatment planning was demonstrated using a large bandwidth sequence and bulk-assigned images. The development of higher quality, low distortion MR sequence will allow regular practice of this technique.

Feasibility Studies↗

PubMed2003

Efficient selective screening of haplotype tag SNPs.

UNLABELLED: Haplotypes defined by common single nucleotide polymorphisms (SNPs) have important implications for mapping of disease genes and human traits. Often only a small subset of the SNPs is sufficient to capture the full haplotype information. Such subsets of markers are called haplotype tagging SNPs (htSNPs). Although htSNPs can be identified by eye, efficient computer algorithms and flexible interactive software tools are required for large datasets such as the human genome haplotype map. We describe a java-based program, SNPtagger, which screens for minimal sets of SNP markers to represent given haplotypes according to various user requirements. The program offers several options for inclusion/exclusion of specific markers and presents alternative panels for final selection. AVAILABILITY: The www-based program is available at http://www.well.ox.ac.uk/~xiayi/haplotype/index.html.

Algorithms↗

PubMed2003

K-ary clustering with optimal leaf ordering for gene expression data.

MOTIVATION: A major challenge in gene expression analysis is effective data organization and visualization. One of the most popular tools for this task is hierarchical clustering. Hierarchical clustering allows a user to view relationships in scales ranging from single genes to large sets of genes, while at the same time providing a global view of the expression data. However, hierarchical clustering is very sensitive to noise, it usually lacks of a method to actually identify distinct clusters, and produces a large number of possible leaf orderings of the hierarchical clustering tree. In this paper we propose a new hierarchical clustering algorithm which reduces susceptibility to noise, permits up to k siblings to be directly related, and provides a single optimal order for the resulting tree. RESULTS: We present an algorithm that efficiently constructs a k-ary tree, where each node can have up to k children, and then optimally orders the leaves of that tree. By combining k clusters at each step our algorithm becomes more robust against noise and missing values. By optimally ordering the leaves of the resulting tree we maintain the pairwise relationships that appear in the original method, without sacrificing the robustness. Our k-ary construction algorithm runs in O(n(3)) regardless of k and our ordering algorithm runs in O(4(k)n(3)). We present several examples that show that our k-ary clustering algorithm achieves results that are superior to the binary tree results in both global presentation and cluster identification. AVAILABILITY: We have implemented the above algorithms in C++ on the Linux operating system.

Algorithms↗

PubMed2006

Refining multiple sequence alignments with conserved core regions.

Accurate multiple sequence alignments of proteins are very important to several areas of computational biology and provide an understanding of phylogenetic history of domain families, their identification and classification. This article presents a new algorithm, REFINER, that refines a multiple sequence alignment by iterative realignment of its individual sequences with the predetermined conserved core (block) model of a protein family. Realignment of each sequence can correct misalignments between a given sequence and the rest of the profile and at the same time preserves the family's overall block model. Large-scale benchmarking studies showed a noticeable improvement of alignment after refinement. This can be inferred from the increased alignment score and enhanced sensitivity for database searching using the sequence profiles derived from refined alignments compared with the original alignments. A standalone version of the program is available by ftp distribution (ftp://ftp.ncbi.nih.gov/pub/REFINER) and will be incorporated into the next release of the Cn3D structure/alignment viewer.

Algorithms↗

PubMed2001

Structure of human uropepsin at 2.45 A resolution.

The molecular structure of human uropepsin, an aspartic proteinase from the urine produced in the form of pepsinogen A in the gastric mucosa, has been determined by molecular replacement using human pepsin as the search model. Crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 50.99, b = 75.56, c = 89.90 A. Crystallographic refinement led to an R factor of 0.161 at 2.45 A resolution. The positions of 2437 non-H protein atoms in 326 residues have been determined and the model contains 143 water molecules. The structure is bilobal, consisting of two predominantly beta-sheet lobes which, as observed in other aspartic proteinases, are related by a pseudo-twofold axis. A model of the uropepsin-pepstatin complex has been constructed based on the high-resolution crystal structure of pepsin complexed with pepstatin.

Amino Acid Sequence↗

PubMed2002

Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction).

BACKGROUND: PCR amplification of bacterial 16S rRNA genes provides the most comprehensive and flexible means of sampling bacterial communities. Sequence analysis of these cloned fragments can provide a qualitative and quantitative insight of the microbial population under scrutiny although this approach is not suited to large-scale screenings. Other methods, such as denaturing gradient gel electrophoresis, heteroduplex or terminal restriction fragment analysis are rapid and therefore amenable to field-scale experiments. A very recent addition to these analytical tools is represented by microarray technology. RESULTS: Here we present our results using a Universal DNA Microarray approach as an analytical tool for bacterial discrimination. The proposed procedure is based on the properties of the DNA ligation reaction and requires the design of two probes specific for each target sequence. One oligo carries a fluorescent label and the other a unique sequence (cZipCode or complementary ZipCode) which identifies a ligation product. Ligated fragments, obtained in presence of a proper template (a PCR amplified fragment of the 16s rRNA gene) contain either the fluorescent label or the unique sequence and therefore are addressed to the location on the microarray where the ZipCode sequence has been spotted. Such an array is therefore "Universal" being unrelated to a specific molecular analysis. Here we present the design of probes specific for some groups of bacteria and their application to bacterial diagnostics. CONCLUSIONS: The combined use of selective probes, ligation reaction and the Universal Array approach yielded an analytical procedure with a good power of discrimination among bacteria.

Bacteria↗

PubMed1991

T1-weighted sequences for MR imaging of the liver: comparison of three techniques for single-breath, whole-volume acquisition at 1.0 and 1.5 T.

The authors compared three T1-weighted magnetic resonance imaging techniques that acquire images encompassing the entire liver in one breath hold. Twenty healthy volunteers were imaged--10 at 1.0 T and 10 at 1.5 T--and the results compared with those of regular short repetition time/echo time spin-echo imaging. Rapid acquisition spin echo was resistant to artifacts and had good image quality but had the lowest liver signal-to-noise (S/N) and spleen-liver signal-difference-to-noise (SD/N) values. Fast low-angle shot (FLASH) had the highest S/N and SD/N, very good image quality, and only mild artifacts. TurboFLASH had good S/N and SD/N, but reduced matrix size decreased image quality. All three sequences had better SD/N than regular spin echo, and FLASH and TurboFLASH had higher S/N. On the basis of this study, the FLASH sequence appears the most attractive for T1-weighted breath-hold imaging.

Adult↗

PubMed2000

An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments.

The information required to generate a protein structure is contained in its amino acid sequence, but how three-dimensional information is mapped onto a linear sequence is still incompletely understood. Multiple structure alignments of similar protein structures have been used to investigate conserved sequence features but contradictory results have been obtained, due, in large part, to the absence of subjective criteria to be used in the construction of sequence profiles and in the quantitative comparison of alignment results. Here, we report a new procedure for multiple structure alignment and use it to construct structure-based sequence profiles for similar proteins. The definition of "similar" is based on the structural alignment procedure and on the protein structural distance (PSD) described in paper I of this series, which offers an objective measure for protein structure relationships. Our approach is tested in two well-studied groups of proteins; serine proteases and Ig-like proteins. It is demonstrated that the quality of a sequence profile generated by a multiple structure alignment is quite sensitive to the PSD used as a threshold for the inclusion of proteins in the alignment. Specifically, if the proteins included in the aligned set are too distant in structure from one another, there will be a dilution of information and patterns that are relevant to a subset of the proteins are likely to be lost. In order to understand better how the same three-dimensional information can be encoded in seemingly unrelated sequences, structure-based sequence profiles are constructed for subsets of proteins belonging to nine superfolds. We identify patterns of relatively conserved residues in each subset of proteins. It is demonstrated that the most conserved residues are generally located in the regions where tertiary interactions occur and that are relatively conserved in structure. Nevertheless, the conservation patterns are relatively weak in all cases studied, indicating that structure-determining factors that do not require a particular sequential arrangement of amino acids, such as secondary structure propensities and hydrophobic interactions, are important in encoding protein fold information. In general, we find that similar structures can fold without having a set of highly conserved residue clusters or a well-conserved sequence profile; indeed, in some cases there is no apparent conservation pattern common to structures with the same fold. Thus, when a group of proteins exhibits a common and well-defined sequence pattern, it is more likely that these sequences have a close evolutionary relationship rather than the similarities having arisen from the structural requirements of a given fold.

Algorithms↗

PubMedDate not supplied

Esophageal magnetic resonance fluoroscopy: optimization of the sequence.

OBJECTIVE: The purpose of this study was to try to delineate the esophageal passage under dynamic conditions and to determine optimum settings for esophageal magnetic resonance (MR) imaging. METHODS: Ten healthy volunteers underwent MR fluoroscopy with two T1-weighted sequences: turbo field echo (TFE) and T1-weighted fast field echo (T1-FFE). These sequences were compared for signal-to-noise ratios (SNRs) and image quality. To determine the optimum slice thickness, an additional 10 healthy volunteers underwent MR fluoroscopy. Results obtained for slice thicknesses of 25, 35, 45, and 55 mm were compared for delineated length of the esophagus and image quality. RESULTS: The T1-FFE sequences provided higher SNRs and better image quality than the TFE sequences (T1-FFE: 89.4 +/- 28.0, TFE: 52.4 +/- 16.7; P < 0.001). Artifacts were less prominent and delineation of the esophageal wall was better on the T1-FFE images. The delineation of the esophageal wall was best with a 35-mm slice thickness, although delineated length was the longest with a 55-mm slice thickness. CONCLUSION: This study showed T1-FFE to be a more suitable sequence than TFE and that the 35-mm slice thickness was the optimum slice thickness for esophageal MR fluoroscopy.

Adult↗

PubMed2004

Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice.

The centromeric retrotransposon (CR) family in the grass species is one of few Ty3-gypsy groups of retroelements that preferentially transpose into highly specialized chromosomal domains. It has been demonstrated in both rice and maize that CRR (CR of rice) and CRM (CR of maize) elements are intermingled with centromeric satellite DNA and are highly concentrated within cytologically defined centromeres. We collected all of the CRR elements from rice chromosomes 1, 4, 8, and 10 that have been sequenced to high quality. Phylogenetic analysis revealed that the CRR elements are structurally diverged into four subfamilies, including two autonomous subfamilies (CRR1 and CRR2) and two nonautonomous subfamilies (noaCRR1 and noaCRR2). The CRR1/CRR2 elements contain all characteristic protein domains required for retrotransposition. In contrast, the noaCRR elements have different structures, containing only a gag or gag-pro domain or no open reading frames. The CRR and noaCRR elements share substantial sequence similarity in regions required for DNA replication and for recognition by integrase during retrotransposition. These data, coupled with the presence of young noaCRR elements in the rice genome and similar chromosomal distribution patterns between noaCRR1 and CRR1/CRR2 elements, suggest that the noaCRR elements were likely mobilized through the retrotransposition machinery from the autonomous CRR elements. Mechanisms of the targeting specificity of the CRR elements, as well as their role in centromere function, are discussed.

Base Sequence↗

PubMed2005

Magnetic resonance cholangiopancreatography: image quality, ductal morphology, and value of additional T2- and T1-weighted sequences for the assessment of suspected pancreatic cancer.

PURPOSE: To assess image quality and duct morphology on magnetic resonance cholangiopancreatography (MRCP) and also the value of additional T2- and T1-weighted sequences for differentiation of benignity and malignancy in patients with suspected pancreatic tumors. MATERIAL AND METHODS: One-hundred-and-fourteen patients received MRCP and unenhanced and contrast material-enhanced MR imaging. MR results were analyzed independently by two blinded readers, and subsequently correlated with the results from surgery, biopsy, and follow-up. Assessment included the evaluation of image quality, duct visualization and morphology, and the differentiation of pancreatic lesion status (benign versus malignant). RESULTS: Overall, 49 patients had benign final diagnoses, while 65 had a malignant diagnosis. Image quality of single-shot thick-slab MRCP was rated significantly better than the MIP images of multisection MRCP. With MRCP alone, the two readers' accuracy in the assessment of pancreatic lesion status was 72% (95% CI, 64% to 83%) and 69% (95% CI, 56% to 77%), respectively; with the addition of T2- and T1-weighted images the accuracy significantly improved to 89% (95% CI, 82% to 95%) and 84% (95% CI, 77% to 92%) for readers 1 and 2, respectively. CONCLUSION: Single-shot thick-slab MRCP and multisection MRCP provide complementary results; however, single-shot MRCP had superior image quality. Moreover, assessment of ductal morphology with MRCP alone facilitated the diagnosis of different pathologic conditions of the pancreatobiliary system in the majority of patients. However, with the addition of T2- and T1-weighted sequences the overall diagnostic accuracy was significantly improved and thus we consider that a comprehensive MR approach should comprise both MRCP techniques and parenchymal sequences.

Adult↗

PubMed1997

Blind predictions of local protein structure in CASP2 targets using the I-sites library.

Blind predictions of the local structure of nine CASP2 targets were made using the I-sites library of short sequence--structure motifs, revealing strengths and weaknesses in this new knowledge-based method. Many turns between secondary structural elements were accurately predicted. Estimates of the confidence of prediction correlated well with the accuracy over the whole set. Bias toward structures used to develop the library was minimal, probably because of the extensive use of cross-validation. However, helix positions were better predicted by the PHD program. The method is likely to be sensitive to the quality of the sequence alignment. A general measure for evaluating local structure predictions is suggested.

Binding Sites↗

PubMed2005

Phylogenetics of modern birds in the era of genomics.

In the 14 years since the first higher-level bird phylogenies based on DNA sequence data, avian phylogenetics has witnessed the advent and maturation of the genomics era, the completion of the chicken genome and a suite of technologies that promise to add considerably to the agenda of avian phylogenetics. In this review, we summarize current approaches and data characteristics of recent higher-level bird studies and suggest a number of as yet untested molecular and analytical approaches for the unfolding tree of life for birds. A variety of comparative genomics strategies, including adoption of objective quality scores for sequence data, analysis of contiguous DNA sequences provided by large-insert genomic libraries, and the systematic use of retroposon insertions and other rare genomic changes all promise an integrated phylogenetics that is solidly grounded in genome evolution. The avian genome is an excellent testing ground for such approaches because of the more balanced representation of single-copy and repetitive DNA regions than in mammals. Although comparative genomics has a number of obvious uses in avian phylogenetics, its application to large numbers of taxa poses a number of methodological and infrastructural challenges, and can be greatly facilitated by a 'community genomics' approach in which the modest sequencing throughputs of single PI laboratories are pooled to produce larger, complementary datasets. Although the polymerase chain reaction era of avian phylogenetics is far from complete, the comparative genomics era-with its ability to vastly increase the number and type of molecular characters and to provide a genomic context for these characters-will usher in a host of new perspectives and opportunities for integrating genome evolution and avian phylogenetics.

Animals↗

PubMed2004

Noise reduction in spine videofluoroscopic images using the undecimated wavelet transform.

Videofluoroscopy permits using sequences of low quality images to study the spine movement. In this work the problem of enhancing the quality of these images is considered in order to facilitate the extraction of kinematic parameters. The method is based on the undecimated wavelet transform and on a preliminary training of a sub-set of images. The anatomical features are preserved using a mask. Key element of the method is its fast and automated implementation. The concept of improving the extraction of kinematic parameters by improving the image representation instead of the technique to extract these is also innovative. The technique has been tested on two sequences of images and the results demonstrates that the method enhances images not related with training sub-set.

Algorithms↗

PubMed1996

Diffusion measurements in the ischemic human brain with a steady-state sequence.

RATIONALE AND OBJECTIVES: The authors evaluate the clinical usefulness of a diffusion-weighted steady-state free-precession (SSFP) sequence to detect acute and subacute ischemic changes. METHODS: Twenty-four patients were examined on a 1.5-tesla scanner, using a SSFP-sequence (repetition time [TR]/ echo time [TE] = 22/3-8 mseconds). The slice thickness was 5 mm, 10 averages, 57 seconds per slice. The diffusion gradient strength was 23 millitesla/m, with b-values from 165 to 598 seconds/mm2. Diffusion-weighted images (DWI) were compared with T2-weighted images. RESULTS: The diffusion-weighted SSFP sequence produced diagnostic quality images in 23 of 24 patients. Diffusion depicted (group 1: 0-12 hours) more acute lesions (3 of 6) than T2-weighted images (2 of 6); the mean lesion diameter depicted by diffusion was 10.9 mm (standard deviation [SD], 12.3) and in T2-weighted images was 4.7 mm (SD 6.8). A significant correlation (P < 0.017) in subacute lesions was found when diffusion was compared with turbo spin echo (mean size difference/T2 = 18.5/17.5 mm, SD 13.2/12.2). CONCLUSIONS: The diffusion-weighted SSFP-sequence is more sensitive in acute ischemia and delineates likewise in subacute ischemia, when compared with T2-weighted imaging.

Adult↗