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At least 433 records · Page 24Linked to original sources

PubMed2004

Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase.

The Tox-Prot program was initiated in order to provide the scientific community a summary of the current knowledge on animal protein toxins. The aim of this program is to systematically annotate all proteins which act as toxins and are produced by venomous and poisonous animals. Venomous animals such as snakes, scorpions, spiders, jellyfish, insects, cone snails, sea anemones, lizards, some fish, and platypus are equipped with a specialized organ to inject venom in their prey. In contrast, poisonous animals such as some fish or worms, lack such organs. Each toxin is annotated according to the quality standards of Swiss-Prot. This means providing a wealth of information that includes the description of the function, domain structure, subcellular location, tissue specificity, variants, similarities to other proteins, keywords, etc. In the framework of this program, particular care has been made to capture what is known on the function and mode of action, posttranslational modifications and 3D structural data which are all relatively abundant in the field of protein toxins. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to Swiss-Prot concerning toxins at Tox-Prot@isb-sib.ch. More information on Tox-Prot can be found at http://www.expasy.org/sprot/tox-prot.

Animals↗

PubMed2000

Genomic exploration of the hemiascomycetous yeasts: 3. Methods and strategies used for sequence analysis and annotation.

The primary analysis of the sequences for our Hemiascomycete random sequence tag (RST) project was performed using a combination of classical methods for sequence comparison and contig assembly, and of specifically written scripts and computer visualization routines. Comparisons were performed first against DNA and protein sequences from Saccharomyces cerevisiae, then against protein sequences from other completely sequenced organisms and, finally, against protein sequences from all other organisms. Blast alignments were individually inspected to help recognize genes within our random genomic sequences despite the fact that only parts of them were available. For each yeast species, validated alignments were used to infer the proper genetic code, to determine codon usage preferences and to calculate their degree of sequence divergence with S. cerevisiae. The quality of each genomic library was monitored from contig analysis of the DNA sequences. Annotated sequences were submitted to the EMBL database, and the general annotation tables produced served as a basis for our comparative description of the evolution, redundancy and function of the Hemiascomycete genomes described in other articles of this issue.

Amino Acid Sequence↗

PubMed2003

New local potential useful for genome annotation and 3D modeling.

A new potential energy function representing the conformational preferences of sequentially local regions of a protein backbone is presented. This potential is derived from secondary structure probabilities such as those produced by neural network-based prediction methods. The potential is applied to the problem of remote homolog identification, in combination with a distance-dependent inter-residue potential and position-based scoring matrices. This fold recognition jury is implemented in a Java application called JThread. These methods are benchmarked on several test sets, including one released entirely after development and parameterization of JThread. In benchmark tests to identify known folds structurally similar to (but not identical with) the native structure of a sequence, JThread performs significantly better than PSI-BLAST, with 10% more structures identified correctly as the most likely structural match in a fold library, and 20% more structures correctly narrowed down to a set of five possible candidates. JThread also improves the average sequence alignment accuracy significantly, from 53% to 62% of residues aligned correctly. Reliable fold assignments and alignments are identified, making the method useful for genome annotation. JThread is applied to predicted open reading frames (ORFs) from the genomes of Mycoplasma genitalium and Drosophila melanogaster, identifying 20 new structural annotations in the former and 801 in the latter.

Animals↗

PubMed1997

Recruitment for controlled clinical trials: literature summary and annotated bibliography.

This article is a literature summary and annotated bibliography of research on recruitment for controlled clinical trials published through 1995. It extends and revises a similar review published in this journal a decade ago. The current commentary focuses on intervening developments in recruitment, including diverse populations, HIV trials, primary prevention trials, recruitment strategies, overall planning and management, patient and physician attitudes, adherence, generalizability, and cost. Profound barriers may exist in the recruitment of diverse populations, involving language, cultural factors, beliefs about medical research, and the appropriateness of available protocols. Extensive literature exists on patient and physician barriers to participation. Trials in HIV-infected or AIDs-diagnosed individuals introduce special considerations, including issues of confidentiality, parallel track design, and populations difficult to define and track. Recruitment strategies such as patient registries, occupational screening, direct mail, and the media are now prominent in the literature. Successful planning and management of an overall recruitment plan include piloting strategies, monitoring recruitment by data tracking systems, and hiring quality staff. Generalizability of study results is influenced by the characteristics of participants and by their adherence to study protocol. With increasingly limited funding to conduct clinical trials, efforts to quantify and reduce recruitment costs are being made. While over 4000 titles were identified, primarily by MEDLINE literature search, the articles summarized emphasize data-supported and -confirmed conclusions, and broad coverage of disease areas. We annotate here 91 outstanding articles useful for formulation of overall recruitment approaches in clinical trials.

Clinical Trials as Topic↗

PubMed2000

The physics of DNA and the annotation of the Plasmodium falciparum genome.

A gene identification procedure is formulated, based on large-scale structural analyses of genomic sequences. The structural property is the physical - thermal - stability of the DNA double-helix, as described by the classical helix-coil model. The analyses are detailed for the Plasmodium falciparum genome, which represents one of the most difficult cases for the gene identification problem (notably because of the extreme AT-richness of the genome). In this genome, the coding domains (either uninterrupted genes or exons in split genes) are accurately identified as regions of high thermal stability. The conclusion is based on the study of the available cloned genes, of which 17 examples are described in detail. These examples demonstrate that the physical criterion is valid for the detection of coding regions whose lengths extend from a few base pairs up to several thousand base pairs. Accordingly, the structural analyses can provide a powerful and convenient tool for the identification of complex genes in the P. falciparum genome. The limits of such a scheme are discussed. The gene identification procedure is applied to the completely sequenced chromosomes (2 and 3), and the results are compared with the database annotations. The structural analyses suggest more or less extensive revision to the annotations, and also allow new putative genes to be identified in the chromosome sequences. Several examples of such new genes are described in detail.

Animals↗

PubMed2002

Mutant laboratory mice with abnormalities in pigmentation: annotated tables.

Mammalian pigment cell research has recently entered a phase of significantly increased activity due largely to the exploitation of the many mutant mouse stocks that are coming on stream. Numerous transgenic, targeted mutagenesis (so-called 'knockouts'), conditional (so-called 'gene switch') and spontaneous mutant mice develop abnormal coat color phenotypes. The number of mice that exhibit such abnormalities is increasing exponentially as genetic engineering methods become routine. Since defined abnormalities in such mutant mice provide important clues to the as yet often poorly understood functional roles of many gene products, this overview includes a corresponding, annotated table of mutant mice with pigmentation alterations. These range from early developmental defects via a large array of coat color abnormalities to a melanoma metastasis model. This overview should provide helpful pointers to investigators who are looking for mouse models to explore or to compare functional activities of genes of interest and for comparing coat color phenotypes of spontaneous or genetically engineered mouse mutants with novel ones. Secondly, this review includes a table of mouse models of specific human diseases with genetically defined pigmentation abnormalities. In summary, this annotated table should serve as a useful reference for anyone interested in the molecular controls of pigmentation.

Animals↗

PubMed2003

Image annotation for conveying automated lung nodule detection results to radiologists.

RATIONALE AND OBJECTIVES: The author investigated the ability of automated techniques to convey the results of an automated lung nodule detection method for human visualization. MATERIALS AND METHODS: Automated nodule detection begins with gray-level thresholding techniques to create a segmented lung volume within which nodule candidates are identified. Morphologic and gray-level features are computed for each candidate. To distinguish between candidates that represent actual nodules and those that represent non-nodules, a rule-based scheme is combined with linear discriminant analysis. For output visualization, final detection results are represented as circles around computer-detected structures in a single section in which each structure appears. Consequently, an inappropriate choice of section could result in an actual nodule detected by the computer but not properly indicated to the radiologist, thus reducing the potential positive impact of that detection on the radiologist's decision-making process. RESULTS: The automated nodule detection method achieved 71% sensitivity with 0.5 false positives per section on 38 CT scans; however, when these results were converted to annotations on the images output for human visualization, only 91% of the computer-detected true-positive nodules received annotations that encompassed a portion of the actual nodule. Thus, the "effective sensitivity" of the automated detection method was reduced. CONCLUSION: The "effective sensitivity" of an automated lung nodule detection system considers the eventual human interaction with system output. Differences between reported computer sensitivity and "effective sensitivity" may be reduced through proper consideration of the assessment of "truth," of the manner in which computer results are scored, and of the complete segmentation of candidates for automated nodule detection.

Diagnosis, Computer-Assisted↗

PubMed1999

Genome annotation: which tools do we have for it?

Genome data have to be converted into knowledge to be useful to biologists. Many valuable computational tools have already been developed to help annotation of plant genome sequences, and these may be improved further, for example by identification of more gene regulatory elements. The lack of a standard computer-assisted annotation platform for eukaryotic genomes remains major bottle-neck.

Arabidopsis↗

PubMed2006

Functional annotation and kinetic characterization of PhnO from Salmonella enterica.

Phosphorus is an essential nutrient for all living organisms. Under conditions of inorganic phosphate starvation, genes from the Pho regulon are induced, allowing microorganisms to use phosphonates as a source of phosphorus. The phnO gene was previously annotated as a transcriptional regulator of unknown function due to sequence homology with members of the GCN5-related N-acyltransferase family (GNAT). PhnO can now be functionally annotated as an aminoalkylphosphonic acid N-acetyltransferase which is able to acetylate a range of aminoalkylphosphonic acids. Studies revealed that PhnO proceeds via an ordered, sequential kinetic mechanism with AcCoA binding first followed by aminoalkylphosphonate. Attack by the amine on the thioester of AcCoA generates the tetrahedral intermediate that collapses to generate the products. The enzyme also requires a divalent metal ion for activity, which is the first example of this requirement for a GNAT family member.

Acetyltransferases↗

PubMedDate not supplied

Real-time pulse oximetry artifact annotation on computerized anaesthetic records.

OBJECTIVES: Adoption of computerised anaesthesia record keeping systems has been limited by the concern that they record artifactual data and accurate data indiscriminately. Data resulting from artifacts does not reflect the patient's true condition and presents a problem in later analysis of the record, with associated medico-legal implications. This study developed an algorithm to automatically annotate pulse oximetry artifacts and sought to evaluate the algorithm's accuracy in routine surgical procedures. METHODS: MacAnaesthetist is a semi-automatic anaesthetic record keeping system developed for the Apple Macintosh computer, which incorporated an algorithm designed to automatically detect pulse oximetry artifacts. The algorithm labeled artifactual oxygen saturation values < 90%. This was done in real-time by analyzing physiological data captured from a Datex AS/3 Anaesthesia Monitor. An observational study was conducted to evaluate the accuracy of the algorithm during routine surgical procedures (n = 20). An anaesthetic record was made by an anaesthetist using the Datex AS/3 record keeper, while a second anaesthetic record was produced in parallel using MacAnaesthetist. A copy of the Datex AS/3 record was kept for later review by a group of anaesthetists (n = 20), who judged oxygen saturation values < 90% to be either genuine or artifact. RESULTS: MacAnaesthetist correctly labeled 12 out of 13 oxygen saturations < 90% (92.3% accuracy). A post-operative review of the Datex AS/3 anaesthetic records (n = 8) by twenty anaesthetists resulted in 127 correct responses out of total of 200 (63.5% accuracy). The remaining Datex AS/3 records (n = 12) were not reviewed, as they did not contain any oxygen saturations <90%. CONCLUSIONS: The real-time artifact detection algorithm developed in this study was more accurate than anaesthetists who post-operatively reviewed records produced by an existing computerised anaesthesia record keeping system. Algorithms have the potential to more accurately identify and annotate artifacts on computerised anaesthetic records, assisting clinicians to more correctly interpret abnormal data.

Algorithms↗

PubMed2001

Mutant laboratory mice with abnormalities in hair follicle morphogenesis, cycling, and/or structure: annotated tables.

Numerous transgenic, targeted mutagenesis (so-called knockouts), conditional (so-called "gene switch") and spontaneous mutant mice develop abnormal hair phenotypes. The number of mice that exhibit such abnormalities is increasing exponentially as genetic engineering methods become routine. Since defined abnormalities in hair follicle morphogenesis, cycling and/or structure in such mutant mice provide important clues to the as yet poorly understood functional roles of many gene products, it is useful to summarize and classify these mutant mice according to their hair phenotype. This review provides a corresponding, annotated table of mutant mice with hair abnormalities, classifying the latter into 6 categories, 1) abnormally low number of hair follicles, 2) disorders of hair morphogenesis, 3) of hair follicle cycling, 4) of hair follicle structure 5) of sebaceous gland structure, and 6) hair growth disorders as a consequence of immunological abnormalities. This annotated table should serve as a useful source of reference for anyone who is interested in the molecular controls of hair growth, for investigators who are looking for mouse models to explore or compare the functional activities of their gene of interest, and for comparing the hair phenotype of newly generated mouse mutants with existing ones.

Animals↗

PubMed2001

Functional annotation of a full-length mouse cDNA collection.

The RIKEN Mouse Gene Encyclopaedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analysed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs extends known gene families and identifies new ones.

Animals↗

PubMed2001

Experimental annotation of the human genome using microarray technology.

The most important product of the sequencing of a genome is a complete, accurate catalogue of genes and their products, primarily messenger RNA transcripts and their cognate proteins. Such a catalogue cannot be constructed by computational annotation alone; it requires experimental validation on a genome scale. Using 'exon' and 'tiling' arrays fabricated by ink-jet oligonucleotide synthesis, we devised an experimental approach to validate and refine computational gene predictions and define full-length transcripts on the basis of co-regulated expression of their exons. These methods can provide more accurate gene numbers and allow the detection of mRNA splice variants and identification of the tissue- and disease-specific conditions under which genes are expressed. We apply our technique to chromosome 22q under 69 experimental condition pairs, and to the entire human genome under two experimental conditions. We discuss implications for more comprehensive, consistent and reliable genome annotation, more efficient, full-length complementary DNA cloning strategies and application to complex diseases.

Algorithms↗

PubMed2006

The DNA sequence and biological annotation of human chromosome 1.

The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.

Base Sequence↗

PubMed2005

Functional genome annotation through phylogenomic mapping.

Accurate determination of functional interactions among proteins at the genome level remains a challenge for genomic research. Here we introduce a genome-scale approach to functional protein annotation--phylogenomic mapping--that requires only sequence data, can be applied equally well to both finished and unfinished genomes, and can be extended beyond single genomes to annotate multiple genomes simultaneously. We have developed and applied it to more than 200 sequenced bacterial genomes. Proteins with similar evolutionary histories were grouped together, placed on a three dimensional map and visualized as a topographical landscape. The resulting phylogenomic maps display thousands of proteins clustered in mountains on the basis of coinheritance, a strong indicator of shared function. In addition to systematic computational validation, we have experimentally confirmed the ability of phylogenomic maps to predict both mutant phenotype and gene function in the delta proteobacterium Myxococcus xanthus.

Bacterial Proteins↗

PubMed2005

Tag-based approaches for transcriptome research and genome annotation.

With the increasing number of whole genome sequences available, genomic research has shifted toward the annotation of functional elements and transcribed regions. Thus, the related field of transcriptome research requires accurate methods for the profiling of genes that are not biased by known sequence information, and that also allow for the identification of promoter regions. Starting with serial analysis of gene expression (SAGE), methods making use of short sequencing tags have greatly contributed to transcriptome studies. Here we review recent developments in the use of short sequencing tags in expression profiling, gene discovery and genome annotation. These tags are obtained from the 5' end of mRNAs, both terminal ends of mRNAs, or genomic regions. The 5' end-specific tags, with their ability to identify transcripts along with their transcriptional start sites, will be of particular interest for gene network studies and may become one of the most important approaches in systems biology.

Animals↗

PubMed2004

Genomic annotation of the meningioma tumor suppressor locus on chromosome 1p34.

Meningioma is a frequently occurring tumor of the meninges surrounding the central nervous system. Loss of the short arm of chromosome 1 (1p) is the second most frequent chromosomal abnormality observed in these tumors. Previously, we identified a 3.7 megabase (Mb) region of consistent deletion on 1p33-p34 in a panel of 157 tumors. Loss of this region was associated with advanced disease and predictive for tumor relapse. In this report, a high-resolution integrated map of the region was constructed (CompView) to identify all markers in the smallest region of overlapping deletion (SRO). A regional somatic cell hybrid panel was used to more precisely localize those markers identified in CompView as within or overlapping the region. Additional deletion mapping using microsatellites localized to the region narrowed the SRO to approximately 2.8 Mb. The 88 markers remaining in the SRO were used to screen genomic databases to identify large-insert clones. Clones were assembled into a physical map of the region by PCR-based, sequence-tagged site (STS) content mapping. A sequence from clones was used to validate STS content by electronic PCR and to identify transcripts. A minimal tiling path of 43 clones was constructed across the SRO. Sequence data from the most current sequence assembly were used for further validation. A total of 59 genes were ordered within the SRO. In all, 17 of these were selected as likely candidates based on annotation using Gene Ontology Consortium terms, including the MUTYH, PRDX1, FOXD2, FOXE3, PTCH2, and RAD54L genes. This annotation of a putative tumor suppressor locus provides a resource for further analysis of meningioma candidate genes.

Chromosomes, Human, Pair 1↗

PubMed2004

Genome annotation by high-throughput 5' RNA end determination.

Complete gene identification and annotation, including alternative transcripts, remains a challenge in understanding genome organization. Such annotation can be achieved by a combination of computational analysis and experimental confirmation. Here, we describe a high-throughput technique, trans-spliced exon coupled RNA end determination (TEC-RED), that identifies 5' ends of expressed genes in nematodes. TEC-RED can distinguish coding regions from regulatory regions and identify genes as well as their alternative transcripts that have different 5' ends. Application of TEC-RED to approximately 10% of the Caenorhabditis elegans genome yielded tags 75% of which experimentally verified predicted 5'-RNA ends and 25% of which provided previously unknown information about 5'-RNA ends, including the identification of 99 previously unknown genes and 32 previously unknown operons. This technique will be applicable in any organisms that have a trans-splicing reaction from spliced leader RNA. We also describe an efficient sequential method for concatenating short sequence tags for any serial analysis of gene expression-like techniques.

Animals↗