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PubMedDate not supplied

Microarray analysis using bioinformatics analysis audit trails (BAATs).

Bioinformatics analysis plays an integrative role in genomics and functional genomics. The ability to conduct quality managed, hypothesis-driven bioinformatics analysis with the plethora of data available is mandatory. Biological interpretation of this data is dependent on versions of databases, programs and the parameters used. Thus, tracking and auditing the analyses process is important. This paper outlines what we term Bioinformatics Analysis Audit Trails (BAATs) and describes YABI, a bioinformatics environment that implements BAATs. YABI can incorporate most bioinformatics tools within the same environment, making it a valuable resource.

Computational Biology↗
PubMed2003

Analysis of the Candida albicans proteome. II. Protein information technology on the Net (update 2002).

Candida albicans is an important fungal model organism of noteworthy clinical interest in modern medicine. Different initiatives addressing its sequencing and physical mapping have been carried out. The C. albicans genome sequence is currently near to completion at Stanford University, heralding new challenges in proteomic research and functional analyses of its gene products. This review presents an update of the most relevant data resources that are available through the World Wide Web to scientists working in the area of the analysis of the C. albicans proteome. An overview of the current status of the main universal protein sequence databases and specialized data collections for C. albicans is given. Various issues of the single public C. albicans 2D-PAGE database are also described, highlighting the significance of setting up graphical query interface-based databanks to visualize 2D-PAGE images through the Net. Finally, we also emphasize the pressing need to create a "cyber-bioknowledge library" that will integrate all the databases developed at the different levels for the understanding of life processes as well as bioinformatic tools for interpreting this deluge of data generated through the Internet.

Candida albicans↗
PubMed2005

Common physical-chemical properties correlate with similar structure of the IgE epitopes of peanut allergens.

Although many sequences and linear IgE epitopes of allergenic proteins have been identified and archived in databases, structural and physicochemical discriminators that define their specific properties are lacking. Current bioinformatics tools for predicting the potential allergenicity of a novel protein use methods that were not designed to compare peptides. Novel tools to determine the quantitative sequence and three-dimensional (3D) relationships between IgE epitopes of major allergens from peanut and other foods have been implemented in the Structural Database of Allergenic Proteins (SDAP; http://fermi.utmb.edu/SDAP/). These peptide comparison tools are based on five-dimensional physicochemical property (PCP) vectors. Sequences from SDAP proteins similar in their physicochemical properties to known epitopes of Ara h 1 and Ara h 2 were identified by calculating property distance (PD) values. A 3D model of Ara h 1 was generated to visualize the 3D structure and surface exposure of the epitope regions and peptides with a low PD value to them. Many sequences similar to the known epitopes were identified in related nut allergens, and others were within the sequences of Ara h 1 and Ara h 2. Some of the sequences with low PD values correspond to other known epitopes. Regions with low PD values to one another in Ara h 1 had similar predicted structure, on opposite sides of the internal dimer axis. The PD scale detected epitope pairs that are similar in structure and/or reactivity with patient IgE. The high immunogenicity and IgE reactivity of peanut allergen proteins might be due to the proteins' arrays of similar antigenic regions on opposite sides of a single protein structure.

2S Albumins, Plant↗
PubMed2006

Current bioinformatics tools in genomic biomedical research (Review).

On the advent of a completely assembled human genome, modern biology and molecular medicine stepped into an era of increasingly rich sequence database information and high-throughput genomic analysis. However, as sequence entries in the major genomic databases currently rise exponentially, the gap between available, deposited sequence data and analysis by means of conventional molecular biology is rapidly widening, making new approaches of high-throughput genomic analysis necessary. At present, the only effective way to keep abreast of the dramatic increase in sequence and related information is to apply biocomputational approaches. Thus, over recent years, the field of bioinformatics has rapidly developed into an essential aid for genomic data analysis and powerful bioinformatics tools have been developed, many of them publicly available through the World Wide Web. In this review, we summarize and describe the basic bioinformatics tools for genomic research such as: genomic databases, genome browsers, tools for sequence alignment, single nucleotide polymorphism (SNP) databases, tools for ab initio gene prediction, expression databases, and algorithms for promoter prediction.

Computational Biology↗
PubMed2005

Bioinformatics toolbox for narrowing rodent quantitative trait loci.

Quantitative trait locus (QTL) analysis is a powerful method for localizing disease genes, but identifying the causal gene remains difficult. Rodent models of disease facilitate QTL gene identification, and causal genes underlying rodent QTL are often associated with the corresponding human diseases. Recently developed bioinformatics methods, including comparative genomics, combined cross analysis, interval-specific and genome-wide haplotype analysis, followed by sequence and expression analysis, each facilitated by public databases, provide new tools for narrowing rodent QTLs. Here we discuss each tool, illustrate its application and generate a bioinformatics strategy for narrowing QTLs. Combining these bioinformatics tools with classical experimental methods should accelerate QTL gene identification.

Animals↗
PubMed2003

Protein family alignment annotation.

For bioscientists studying protein structure and function, the Protein Family Alignment Annotation Tool (Pfaat) is a useful and simple program for annotating collections of proteins. This open-source software includes methods for viewing and aligning protein families, and for annotating sequence structure and residues with known functions. It offers new options to aid the study of proteins, and an extensible annotation tool for bioinformatics developers.

Amino Acid Sequence↗
PubMed2006

A Web-based assessment of bioinformatics end-user support services at US universities.

OBJECTIVES: This study was conducted to gauge the availability of bioinformatics end-user support services at US universities and to identify the providers of those services. The study primarily focused on the availability of short-term workshops that introduce users to molecular biology databases and analysis software. METHODS: Websites of selected US universities were reviewed to determine if bioinformatics educational workshops were offered, and, if so, what organizational units in the universities provided them. RESULTS: Of 239 reviewed universities, 72 (30%) offered bioinformatics educational workshops. These workshops were located at libraries (N = 15), bioinformatics centers (N = 38), or other facilities (N = 35). No such training was noted on the sites of 167 universities (70%). Of the 115 bioinformatics centers identified, two-thirds did not offer workshops. CONCLUSIONS: This analysis of university Websites indicates that a gap may exist in the availability of workshops and related training to assist researchers in the use of bioinformatics resources, representing a potential opportunity for libraries and other facilities to provide training and assistance for this growing user group.

Computational Biology↗
PubMed2000

An ontology for biological function based on molecular interactions.

MOTIVATIONS: A number of important bioinformatics computations involve computing with function: executing computational operations whose inputs or outputs are descriptions of the functions of biomolecules. Examples include performing functional queries to sequence and pathway databases, and determining functional equality to evaluate algorithms that predict function from sequence. A prerequisite to computing with function is the existence of an ontology that provides a structured semantic encoding of function. Functional bioinformatics is an emerging subfield of bioinformatics that is concerned with developing ontologies and algorithms for computing with biological function. RESULTS: The article explores the notion of computing with function, and explains the importance of ontologies of function to bioinformatics. The functional ontology developed for the EcoCyc database is presented. This ontology can encode a diverse array of biochemical processes, including enzymatic reactions involving small-molecule substrates and macromolecular substrates, signal-transduction processes, transport events, and mechanisms of regulation of gene expression. The ontology is validated through its use to express complex functional queries for the EcoCyc DB. CONTACT: pkarp@ai.sri.com

Computational Biology↗
PubMed2000

Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors.

MOTIVATION: Sequence database searching is among the most important and challenging tasks in bioinformatics. The ultimate choice of sequence-search algorithm is that of Smith-Waterman. However, because of the computationally demanding nature of this method, heuristic programs or special-purpose hardware alternatives have been developed. Increased speed has been obtained at the cost of reduced sensitivity or very expensive hardware. RESULTS: A fast implementation of the Smith-Waterman sequence-alignment algorithm using Single-Instruction, Multiple-Data (SIMD) technology is presented. This implementation is based on the MultiMedia eXtensions (MMX) and Streaming SIMD Extensions (SSE) technology that is embedded in Intel's latest microprocessors. Similar technology exists also in other modern microprocessors. Six-fold speed-up relative to the fastest previously known Smith-Waterman implementation on the same hardware was achieved by an optimized 8-way parallel processing approach. A speed of more than 150 million cell updates per second was obtained on a single Intel Pentium III 500 MHz microprocessor. This is probably the fastest implementation of this algorithm on a single general-purpose microprocessor described to date.

Algorithms↗
PubMed2003

MASV--Multiple (BLAST) Annotation System Viewer.

UNLABELLED: Multiple (BLAST) Annotation System Viewer (MASV) is a tool designed to aid in the annotation of genomic sequences. MASV enables the researcher to compare and analyse differences in annotation and analysis, resulting from changes in databases, analysis program parameters and results. This provides a unique capability for the user to conduct further bioinformatics analysis from the information obtained. AVAILABILITY: http://cbbc.murdoch.edu.au/projects/masv/

Abstracting and Indexing↗
PubMed1998

The human gene mutation database.

The Human Gene Mutation Database (HGMD) represents a comprehensive core collection of data on published germline mutations in nuclear genes underlying human inherited disease. By September 1997, the database contained nearly 12 000 different lesions in a total of 636 different genes, with new entries currently accumulating at a rate of over 2000 per annum. Although originally established for the scientific study of mutational mechanisms in human genes, HGMD has acquired a much broader utility to researchers, physicians and genetic counsellors so that it was made publicly available at http://uwcm.ac.uk/uwcm/mg/hgmd0.html in April 1996. Mutation data in HGMD are accessible on the basis of every gene being allocated one web page per mutation type, if data of that type are present. Meaningful integration with phenotypic, structural and mapping information has been accomplished through bi-directional links between HGMD and both the Genome Database (GDB) and Online Mendelian Inheritance in Man (OMIM), Baltimore, USA. Hypertext links have also been established to Medline abstracts through Entrez , and to a collection of 458 reference cDNA sequences also used for data checking. Being both comprehensive and fully integrated into the existing bioinformatics structures relevant to human genetics, HGMD has established itself as the central core database of inherited human gene mutations.

Computer Communication Networks↗
PubMed2000

MIPS: a database for genomes and protein sequences.

The Munich Information Center for Protein Sequences (MIPS-GSF), Martinsried, near Munich, Germany, continues its longstanding tradition to develop and maintain high quality curated genome databases. In addition, efforts have been intensified to cover the wealth of complete genome sequences in a systematic, comprehensive form. Bioinformatics, supporting national as well as European sequencing and functional analysis projects, has resulted in several up-to-date genome-oriented databases. This report describes growing databases reflecting the progress of sequencing the Arabidopsis thaliana (MATDB) and Neurospora crassa genomes (MNCDB), the yeast genome database (MYGD) extended by functional analysis data, the database of annotated human EST-clusters (HIB) and the database of the complete cDNA sequences from the DHGP (German Human Genome Project). It also contains information on the up-to-date database of complete genomes (PEDANT), the classification of protein sequences (ProtFam) and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database. These databases can be accessed through the MIPS WWW server (http://www. mips.biochem.mpg.de).

Arabidopsis↗
PubMed2006

[Bioinformatic analysis of adenoma-normal mucosa SSH library of colon].

We established a colonic adenoma-normal mucosa suppressive subtraction hybridization (SSH) library in 1999. In this study, we wanted to explore the expression profile of all candidate genes in this library. We developed an EST pipeline which contained two in-house software packages, nucleic acid analytical software and GetUni. The nucleic acid analytical software, an integrator of the universal bioinformatics tools including phred, phd2fasta, cross_match, repeatmasker and blast2.0, can blast sequences of differential clones with the downloaded non-redundant nucleotide (NR) database. GetUni can cluster these NR sequences into Unigene via matching with the downloaded Homo Sapiens UniGene database. Sixty-two candidate genes in A-N library were obtained via the high throughput automatic gene expression bioinformatics pipeline. Gene Ontology online analysis revealed that ribosome genes and immunity-regulating genes were the two most common categories in the KEGG or Biocarta Pathway. We also detected the expression of 2 genes with highest hits, Reg4 and FAM46A, by semi-quantitative RT-PCR. Both genes were up-regulated in 10 or 9 out of 10 adenomas in comparison with the paired normal mucosa, respectively. The candidate genes in A-N library would be of great significance in disclosing the molecular mechanism underlying in colonic adenoma initiation and progression.

Adenoma↗
PubMed2002

An integrated database of chemosensitivity to 55 anticancer drugs and gene expression profiles of 39 human cancer cell lines.

To explore genes that determine the sensitivity of cancer cells to anticancer drugs, we investigated using cDNA microarrays the expression of 9216 genes in 39 human cancer cell lines pharmacologically characterized on treatment with various anticancer drugs. A bioinformatical approach was then exploited to identify genes related to anticancer drug sensitivity. An integrated database of gene expression and drug sensitivity profiles was constructed and used to identify genes with expression patterns that showed significant correlation to patterns of drug responsiveness. As a result, sets of genes were extracted for each of the 55 anticancer drugs examined. Whereas some genes commonly correlated with various classes of anticancer drugs, other genes correlated only with specific drugs with similar mechanisms of action. This latter group of genes may reflect the efficacy of each class of drugs. Therefore, the integrated database approach of gene expression and chemosensitivity profiles may be useful in the development of systems to predict drug efficacies of cancer cells by examining the expression levels of particular genes.

Antineoplastic Agents↗
PubMed2006

QSCOP--SCOP quantified by structural relationships.

UNLABELLED: The database SCOP (Structural Classification Of Proteins) has become a major resource in bioinformatics and protein science. A particular strength of SCOP is the flexibility of its rules enabling the preservation of the many details spotted by experts in the classification process. Here we endow classic SCOP Families with quantified structural information and comment on the structural diversity found in the SCOP hierarchy. AVAILABILITY: Quantified SCOP (QSCOP) is available as a public WEB service. http://services.came.sbg.ac.at.

Computer Simulation↗