Search and retrieve. Large-scale data generation is becoming increasingly important in biological research. But how good are the tools to make sense of the data?
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Computational Biology↗
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Results for “Data Storage And Retrieval”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
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Data compression in a textual medical application.
On-line storage of textual data can represent a significant expense even with today's lower storage costs. This paper presents a hybrid compression scheme designed for rapid decoding and retrieval in a medical data base application. Utilizing this method, a 60% reduction of the space required has been obtained.
Computers↗
Data management and analysis for gene expression arrays.
Microarray technology makes it possible to simultaneously study the expression of thousands of genes during a single experiment. We have developed an information system, ArrayDB, to manage and analyse large-scale expression data. The underlying relational database was designed to allow flexibility in the nature and structure of data input and also in the generation of standard or customized reports through a web-browser interface. ArrayDB provides varied options for data retrieval and analysis tools that should facilitate the interpretation of complex hybridization results. A sampling of ArrayDB storage, retrieval and analysis capabilities is available (www.nhgri.nih.gov/DIR/LCG/15K/HTML/ ), along with information on a set of approximately 15,000 genes used to fabricate several widely used microarrays. Information stored in ArrayDB is used to provide integrated gene expression reports by linking array target sequences with NCBI's Entrez retrieval system, UniGene and KEGG pathway views. The integration of external information resources is essential in interpreting intrinsic patterns and relationships in large-scale gene expression data.
Computer Communication Networks↗
PALIREL, a computer program for analyzing particle-to-membrane relations, with emphasis on electron micrographs of immunocytochemical preparations and gold labeled molecules.
Many vital substances, such as receptors, transporters, and ion channels, in cells occur associated with membranes. To an increasing extent their precise localization is demonstrated by immunocytochemical methods including labeling with gold particles followed by electron microscopy. PALIREL has primarily been developed to facilitate such research, enabling rapid analysis of topographic relations of particles (gold or others) to neighboring linear interfaces (membranes). After digitization of membranes and particles, the program particularly allows computation of (1) the particle number and number per unit length of membrane, in individual bins (membrane lengths) interactively defined along the membrane; (2) the distance of each particle from the membrane; (3) the particle number, and the density (number per micron2), in zones defined along (over and under) the membrane; and (4) the particle number and density in "zonebins" resulting from zones and bins being defined simultaneously. If there occurs, somewhere in the membrane, a segment of different nature, such as a synapse, the quantitative data may be had separately for that and the adjoining parts of the membrane. PALIREL allows interactive redefinition of bins, zones, or objects (particle-line files) while other definitions are retained. The results can be presented on the screen as tables and histograms and be printed on request. A dedicated graphic routine permits inspection on screen of lines, particles, zones, and bins. PALIREL is equally applicable to biological investigations of other kinds, in which the topographic relations of points (structures represented as points) to lines (boundaries) are to be examined. PALIREL is available from the authors on a noncommercial basis.
Algorithms↗
Integrating digital radiography: from diagnostic input to procedure guidance.
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Computer Systems↗
Motifer, a search tool for finding amino acid sequence patterns from nucleotide sequence databases.
Motifer is a software tool able to find directly in nucleotide databases very distant homologues to an amino acid query sequence. It focuses searches on a specific amino acid pattern, scoring the matching and intervening residues as specified by the user. The program has been developed for searching databases of expressed sequence tags (ESTs), but it is also well suited to search genomic sequences. The query sequence can be a variable pattern with alternative amino acids or gaps and the sequences searched can contain introns or sequencing errors with accompanying frame shifts. Other features include options to generate a searchable output, set the maximal sequencing error frequency, limit searches to given species, or exclude already known matches. Motifer can find sequence homologues that other search algorithms would deem unrelated or would not find because of sequencing errors or a too large number of other homologues. The ability of Motifer to find relatives to a given sequence is exemplified by searches for members of the transforming growth factor-beta family and for proteins containing a WW-domain. The functions aimed at enhancing EST searches are illustrated by the 'in silico' cloning of a novel cytochrome P450 enzyme.
Amino Acid Sequence↗
The Protein Data Bank and the challenge of structural genomics.
The PDB has created systems for the processing, exchange, query, and distribution of data that will enable many aspects of high throughput structural genomics.
Computational Biology↗
A uniform proteomics MS/MS analysis platform utilizing open XML file formats.
The analysis of tandem mass (MS/MS) data to identify and quantify proteins is hampered by the heterogeneity of file formats at the raw spectral data, peptide identification, and protein identification levels. Different mass spectrometers output their raw spectral data in a variety of proprietary formats, and alternative methods that assign peptides to MS/MS spectra and infer protein identifications from those peptide assignments each write their results in different formats. Here we describe an MS/MS analysis platform, the Trans-Proteomic Pipeline, which makes use of open XML file formats for storage of data at the raw spectral data, peptide, and protein levels. This platform enables uniform analysis and exchange of MS/MS data generated from a variety of different instruments, and assigned peptides using a variety of different database search programs. We demonstrate this by applying the pipeline to data sets generated by ThermoFinnigan LCQ, ABI 4700 MALDI-TOF/TOF, and Waters Q-TOF instruments, and searched in turn using SEQUEST, Mascot, and COMET.
Archaeal Proteins↗
Organization of data input--the importance of rapid/high quality data collection.
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Data Collection↗
XML: sharing occupational health data in the information age.
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Data Collection↗
Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae.
MOTIVATION: We demonstrate a computational process by which transcription factor binding sites can be elucidated using genome-wide expression and binding profiles. The profiles direct us to the intergenic locations likely to contain the promoter regions for a given factor. These sequences are multiply and locally aligned to give an anchor motif from which further characterization can take place. RESULTS: We present bases for and assumptions about the variability within these motifs which give rise to potentially more accurate motifs, capture complex binding sites built upon the basis motif, and eliminate the constraints of the currently employed promoter searching protocols. We also present a measure of motif quality based on the occurrence of the putative motifs in regions observed to contain the binding sites. The assumptions, motif generation, quality assessment and comparison allow the user as much control as their a priori knowledge allows. AVAILABILITY: IGRDB and the datasets mentioned herein are available at http://chipdb.wi.mit.edu/
Amino Acid Motifs↗
PCR designer for restriction analysis of various types of sequence mutation.
Restriction analysis is widely used to detect gene mutations such as insertions, deletions and single nucleotide polymorphisms (SNPs). Although such mutation sites sometimes present some natural restriction sites to differentiate the wild-type and mutant sequences, mismatches are often needed in order to create artificial restriction fragment length polymorphisms (RFLPs). In this report, a computer program is described that screens for suitable restriction enzymes, introducing mismatches where appropriate and when necessary, designs primers using the information of the selected restriction enzymes, their recognition sequence and locations as well as the information about the mismatches if any. The program, supported by a WWW web interface, is intended to be used online.
Amidohydrolases↗
STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification.
MOTIVATION: Evolutionary relationships of proteins have long been derived from the alignment of protein sequences. But from the view of function, most restraints of evolutionary divergence operate at the level of tertiary structure. It has been demonstrated that quantitative measures of dissimilarity in families of structurally similar proteins can be applied to the construction of trees from a comparison of their three-dimensional structures. However, no convenient tool is publicly available to carry out such analyses. RESULTS: We developed STRUCLA (STRUcture CLAssification), a WWW tool for generation of trees based on evolutionary distances inferred from protein structures according to various methods. The server takes as an input a list of PDB files or the initial alignment of protein coordinates provided by the user (for instance exported from SWISS PDB VIEWER). The user specifies the distance cutoff and selects the distance measures. The server returns series of unrooted trees in the NEXUS format and corresponding distance matrices, as well as a consensus tree. The results can be used as an alternative and a complement to a fixed hierarchy of current protein structure databases. It can complement sequence-based phylogenetic analysis in the 'twilight zone of homology', where amino acid sequences are too diverged to provide reliable relationships.
Algorithms↗
Modeling sequencing errors by combining Hidden Markov models.
Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts but for technical reasons they often contain sequencing errors. Therefore, when analyzing EST sequences computationally, such errors must be taken into account. Earlier attempts to model error prone coding regions have shown good performance in detecting and predicting these while correcting sequencing errors using codon usage frequencies. In the research presented here, we improve the detection of translation start and stop sites by integrating a more complex mRNA model with codon usage bias based error correction into one hidden Markov model (HMM), thus generalizing this error correction approach to more complex HMMs. We show that our method maintains the performance in detecting coding sequences.
Algorithms↗
Soap-HT-BLAST: high throughput BLAST based on Web services.
SUMMARY: A high throughput Basic Local Alignment Search Tool (BLAST) system based on Web services is implemented. It provides an alternative BLAST service and allows users to perform multiple BLAST queries at one run in a distributed, parallel environment through the Internet. AVAILABILITY: It is available at http://mammoth.bii.a-star.edu.sg/webservices/htblast/index.html and at http://www.bii.a-star.edu.sg/jiren/download.html
Amino Acid Sequence↗
Parallel BLAST on split databases.
SUMMARY: BLAST programs often run on large SMP machines where multiple threads can work simultaneously and there is enough memory to cache the databases between program runs. A group of programs is described which allows comparable performance to be achieved with a Beowulf configuration in which no node has enough memory to cache a database but the cluster as an aggregate does. To achieve this result, databases are split into equal sized pieces and stored locally on each node. Each query is run on all nodes in parallel and the resultant BLAST output files from all nodes merged to yield the final output. AVAILABILITY: Source code is available from ftp://saf.bio.caltech.edu/
Amino Acid Sequence↗
UniProt archive.
UniProt Archive (UniParc) is the most comprehensive, non-redundant protein sequence database available. Its protein sequences are retrieved from predominant, publicly accessible resources. All new and updated protein sequences are collected and loaded daily into UniParc for full coverage. To avoid redundancy, each unique sequence is stored only once with a stable protein identifier, which can be used later in UniParc to identify the same protein in all source databases. When proteins are loaded into the database, database cross-references are created to link them to the origins of the sequences. As a result, performing a sequence search against UniParc is equivalent to performing the same search against all databases cross-referenced by UniParc. UniParc contains only protein sequences and database cross-references; all other information must be retrieved from the source databases.
Amino Acid Sequence↗
BlastAlign: a program that uses blast to align problematic nucleotide sequences.
UNLABELLED: BlastAlign uses NCBI blastn to build a multiple nucleotide alignment and is intended for use with sequences that have large indels or are otherwise difficult to align globally. The program builds a matrix representing regions of homology along the sequences, from which it selects the 'most representative' sequence and then extracts the blastn query-anchored multiple alignment for this sequence. The matrix is printed and allows subgroups to be identified visually and an option allows other sequences to be used as the 'most representative'. The program contains elements of both Perl and Python and will run on UNIX (including Mac OSX) and DOS. An additional Perl program BlastAlignP uses tblastn to align nucleotide sequences to a single amino acid sequence, thus allowing an open reading frame to be maintained in the resulting multiple alignment. AVAILABILITY: It is freely available at http://www.bio.ic.ac.uk/research/belshaw/BlastAlign.tar and at http://evolve.zoo.ox.ac.uk/software/blastalign.
Algorithms↗