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PubMed1998

Identification of a novel human glutathione S-transferase using bioinformatics.

In searching the expressed sequence tag (EST) data-base of GenBank with coding sequences of 11 known human glutathione S-transferases in conjunction with bioinformatic analysis, we have identified five ESTs that encode a new human glutathione S-transferase (GST) designated GST A4. The cDNA clone (I.M.A.G.E. Consortium cDNA Clone ID 515157) had an insert length of 1279 bp and contains an open reading frame of 666 bp, which encodes a protein of 222 amino acid residues. The GST A4 protein is identical in length to human GST A1 and A2 and is 54% identical to human GST A1 and A2. Sequence comparison with other human GSTs suggests that it is a new GST belonging to the alpha class GSTs. Northern blot analysis and EST database searches have demonstrated that the GST A4 mRNA is expressed at a high level in brain, placenta, and skeletal muscle and much lower in lung and liver. Analysis of the sequence tagged site (STS) database indicated that the GST A4 gene is located on chromosome 6. This STS represents a previously unidentified transcript further confirming the novelty of the new sequence.

Amino Acid Sequence↗

PubMed2005

Improved classification of mass spectrometry database search results using newer machine learning approaches.

Manual analysis of mass spectrometry data is a current bottleneck in high throughput proteomics. In particular, the need to manually validate the results of mass spectrometry database searching algorithms can be prohibitively time-consuming. Development of software tools that attempt to quantify the confidence in the assignment of a protein or peptide identity to a mass spectrum is an area of active interest. We sought to extend work in this area by investigating the potential of recent machine learning algorithms to improve the accuracy of these approaches and as a flexible framework for accommodating new data features. Specifically we demonstrated the ability of boosting and random forest approaches to improve the discrimination of true hits from false positive identifications in the results of mass spectrometry database search engines compared with thresholding and other machine learning approaches. We accommodated additional attributes obtainable from database search results, including a factor addressing proton mobility. Performance was evaluated using publically available electrospray data and a new collection of MALDI data generated from purified human reference proteins.

Amino Acid Sequence↗

PubMed2000

MPBLAST : improved BLAST performance with multiplexed queries.

UNLABELLED: We have developed a program, MPBLAST, that increases the throughput of batch BLASTN searches by multiplexing (concatenating) query sequences and thereby reducing the number of actual database searches performed. Throughput was observed to increase in reciprocal proportion to the component sequence length. For sequencing read-sized queries of 500 bp, an order of magnitude speed-up was seen. AVAILABILITY: Free (see http://blast.wustl.edu) CONTACT: [ikorf, gish]@watson.wustl.edu

Computational Biology↗

PubMed2005

Mediator-lipidomics: databases and search algorithms for PUFA-derived mediators.

Lipid mediators (LMs) derived from PUFAs play important roles in health and disease. Databases and search algorithms are crucial, but currently unavailable, for accurate and prompt analysis of LMs via liquid chromatography-ultraviolet-tandem mass spectrometry (LC-UV-MS/MS). A novel algorithm and databases, cognoscitive-contrast-angle algorithm and databases (COCAD), were developed for the identification of LMs based on the integration of standard MS/MS spectra with chromatograms and UV spectra. Segment naming and empirical fragmentation rules were introduced to determine MS/MS ion identities, along with ion intensities used by COCAD in matching the unknown to those of authentic standards. The structures of potential LMs without synthetic and/or authentic products as standards were identified by developing theoretical databases and algorithms based on virtual LC-UV-MS/MS spectra and chromatograms. The performance of these databases and algorithms was tested by identifying LMs in murine tissues. These results indicate that COCAD has many advantages for profiling and identification of LMs compared with the conventional dot-product algorithm.

Algorithms↗

PubMed2002

TAD: a web interface and database for tissue microarrays.

Tissue microarrays are increasingly important tools that bring high-throughput technology to traditional pathology laboratories. In many cases, each spot on a tissue microarray is scored by a skilled pathologist and recorded manually. TAD consists of an Active Server Page web interface to a relational database that automates recording scores and linking them with clinical data for future interpretation. TAD is an open source application that can be installed locally.

Computational Biology↗

PubMedDate not supplied

Designing multiple simultaneous seeds for DNA similarity search.

The challenge of similarity search in massive DNA sequence databases has inspired major changes in BLAST-style alignment tools, which accelerate search by inspecting only pairs of sequences sharing a common short "seed," or pattern of matching residues. Some of these changes raise the possibility of improving search performance by probing sequence pairs with several distinct seeds, any one of which is sufficient for a seed match. However, designing a set of seeds to maximize their combined sensitivity to biologically meaningful sequence alignments is computationally difficult, even given recent advances in designing single seeds. This work describes algorithmic improvements to seed design that address the problem of designing a set of n seeds to be used simultaneously. We give a new local search method to optimize the sensitivity of seed sets. The method relies on efficient incremental computation of the probability that an alignment contains a match to a seed pi, given that it has already failed to match any of the seeds in a set Pi. We demonstrate experimentally that multi-seed designs, even with relatively few seeds, can be significantly more sensitive than even optimized single-seed designs.

Algorithms↗

PubMed2005

A distributed computation of Interpro Pfam, PROSITE and ProDom for protein annotation.

Interpro is a widely used tool for protein annotation in genome sequencing projects, demanding a large amount of computation and representing a huge time-consuming step. We present a strategy to execute programs using databases Pfam, PROSITE and ProDom of Interpro in a distributed environment using a Java-based messaging system. We developed a two-layer scheduling architecture of the distributed infrastructure. Then, we made experiments and analyzed the results. Our distributed system gave much better results than Interpro Pfam, PROSITE and ProDom running in a centralized platform. This approach seems to be appropriate and promising for highly demanding computational tools used for biological applications.

Computational Biology↗

PubMed2001

A novel method for sampling alpha-helical protein backbones.

We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically possible three-dimensional arrangements of the constituent helices. We produce a library of possible folds for 25 helical protein cores. In each case, our method finds significant numbers of conformations close to the native structure. In addition, we assign coordinates to all atoms for four of the 25 proteins and show that this has a small effect on the number of near-native conformations. In the context of database driven exhaustive enumeration our method performs extremely well, yielding significant percentages of conformations (between 0.02% and 82%) within 6 A of the native structure. The method's speed and efficiency make it a valuable tool for predicting protein structure.

Amino Acid Sequence↗

PubMedDate not supplied

DBParser: web-based software for shotgun proteomic data analyses.

We describe a web-based program called 'DBParser' for rapidly culling, merging, and comparing sequence search engine results from multiple LC-MS/MS peptide analyses. DBParser employs the principle of parsimony to consolidate redundant protein assignments and derive the most concise set of proteins consistent with all of the assigned peptide sequences observed in an experiment or series of experiments. The resulting reports summarize peptide and protein identifications from multidimensional experiments that may contain a single data set or combine data from a group of data sets, all related to a single analytical sample. Additionally, the results of multiple experiments, each of which may contain several data sets, can be compared in reports that identify features that are common or different. DBParser actively links to the primary mass spectral data and to public online databases such as NCBI, GO, and Swiss-Prot in order to structure contextually specific reports for biologists and biochemists.

Amino Acid Sequence↗

PubMed2003

From knowing to controlling: a path from genomics to drugs using small molecule probes.

The National Cancer Institute Initiative in Chemical Genetics is designed to encourage the development of small molecular probes. The probes are useful for activating or inactivating protein functions, thereby providing resources that help discern the functions of gene products in normal and disease cells, as well as in tissues. This initiative includes "ChemBank," a suite of informatics tools and databases aimed at promoting the development and use of chemical genetics by scientists worldwide. The information generated with such tools should provide a critical link from genomic discovery to drug development.

Animals↗

PubMed2006

[The informatics of human genome and traditional Chinese medicine].

Guided by the theory and methodology of yin-yang set derived from Changing Book and Medicine Canon, and using genetics as a bridge, we have tried to bring together the ancient functional systematology and modern structural one as well as Eastern and Western medicine, thereby promoting the modernization of traditional Chinese medicine (TCM) in theory and in clinical practice. Herein, we used virtual technology to transform the genetic information in OMIM of NCBI (National Center for Biotechnology Information of USA, http://www.ncbi.nlm.nih.gov ) into a secondary database in the form of webpages. There are sixteen kinds of the database named gene morbidity ones as followings as: the nature of gene, the profile of common phenotype, a interaction of endogenous, the disease of a organ or a viscera pathogenesis phenomenon, TCM, the sign of diagnosis of western medicine, the gene response to environment, syndrome, disease, nerve and -endocrine, tumor and cancer, psychology and behavior, morbidity, endo-factor of molecular information, expression, the interaction between endogenous and exogenous in which there is 4 711 words, files. The advantages of the database are its aptness for using human fuzzy intelligence to recognize things, suitability to uncovering the noumenon (yinyang) nature of an object and applicability to clinical use.

Computational Biology↗

PubMed2005

Confident protein identification using the average peptide score method coupled with search-specific, ab initio thresholds.

Perhaps the greatest difficulty in interpreting large sets of protein identifications derived from mass spectrometric methods is whether or not to trust the results. For such experiments, the level of confidence in each protein identification made needs to be far greater than the often used 95% significance threshold to avoid the identification of many false-positives. To provide higher confidence results, we have developed an innovative scoring strategy coupling the recently published Average Peptide Score (APS) method with pre-filtering of peptide identifications, using a simple peptide quality filter. Iterative generation of these filters in conjunction with reversed database searching is used to determine the correct levels at which the APS and peptide quality thresholds should be set to return virtually zero false-positive reports. This proceeds without the need to reference a known dataset.

Computational Biology↗

PubMed2006

Reconsidering the human immunoglobulin heavy-chain locus: 1. An evaluation of the expressed human IGHD gene repertoire.

We have used a bioinformatics approach to evaluate the completeness and functionality of the reported human immunoglobulin heavy-chain IGHD gene repertoire. Using the hidden Markov-model-based iHMMune-align program, 1,080 relatively unmutated heavy-chain sequences were aligned against the reported repertoire. These alignments were compared with alignments to 1,639 more highly mutated sequences. Comparisons of the frequencies of gene utilization in the two databases, and analysis of features of aligned IGHD gene segments, including their length, the frequency with which they appear to mutate, and the frequency with which specific mutations were seen, were used to determine the reliability of alignments to the less commonly seen IGHD genes. Analysis demonstrates that IGHD4-23 and IGHD5-24, which have been reported to be open reading frames of uncertain functionality, are represented in the expressed gene repertoire; however, the functionality of IGHD6-25 must be questioned. Sequence similarities make the unequivocal identification of members of the IGHD1 gene family problematic, although all genes except IGHD1-14*01 appear to be functional. On the other hand, reported allelic variants of IGHD2-2 and of the IGHD3 gene family appear to be nonfunctional, very rare, or nonexistent. Analysis also suggests that the reported repertoire is relatively complete, although one new putative polymorphism (IGHD3-10*p03) was identified. This study therefore confirms a surprising lack of diversity in the available IGHD gene repertoire, and restriction of the germline sequence databases to the functional set described here will substantially improve the accuracy of IGHD gene alignments and therefore the accuracy of analysis of the V-D-J junction.

Alleles↗

PubMed2000

IMpRH server: an RH mapping server available on the Web.

SUMMARY: The INRA-Minnesota Porcine Radiation Hybrid (IMpRH) Server provides both a mapping tool (IMpRH mapping tool) and a database (IMpRH database) of officially submitted results. The mapping tool permits the mapping of a new marker relatively to markers previously mapped on the IMpRH panel. The IMpRH database is the official database for submission of new results and queries. The database not only permits the sharing of public data but also semi-private and private data.

Animals↗

PubMed2005

PRECISE: software for prediction of cis-acting regulatory elements.

The regulation of gene expression at the transcription initiation level is highly complex and requires the presence of multiple transcription factors. These transcription factors are often proteins or peptides that bind to the so-called cis-acting elements, which are present in the promoter regions and conserved among different species. In order to predict these cis-acting elements, a computer program called PRECISE (Prediction of REgulatory CIS-acting Elements) was developed. The power of the tool lies in its user-friendly interface and in the possibility of using empirical motif frequency tables to filter through the many discovered motifs. The tools to create the empirical motif frequency table (e.g., from a whole genome sequence) are included in the package. In the first case study, the upstream regions of all the genes in the Arabidopsis genome were used to create an empirical motif frequency table and a set of 64 upstream sequences of genes known to be involved in starch metabolism was subjected to analysis by PRECISE. The 20 motifs with the highest specificity in the selected set were analyzed in more detail. Of these 20 motifs, 15 showed a very high or complete homology to the sequences of known cis-acting elements. These cis-acting elements are regulated by light, auxin, and abscisic acid, and confer specific expression in sink organs such as leaves and seeds. All these factors have been shown to play an important role in starch biosynthesis. In the second case study, the upstream regions of 16 genes whose transcription is induced by gibberellins (GA) in Arabidopsis were analyzed with PRECISE and compared to the motifs present in the PLACE database. Among the most promising motifs found by PRECISE were 6 of the 17 known GA motifs. These results indicate the power of the PRECISE software package in the prediction of regulatory elements.

Algorithms↗

PubMed2004

coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics.

We have constructed coliBASE, a database for Escherichia coli, Shigella and Salmonella comparative genomics available online at http://colibase. bham.ac.uk. Unlike other E.coli databases, which focus on the laboratory model strain K12, coliBASE is intended to reflect the full diversity of E.coli and its relatives. The database contains comparative data including whole genome alignments and lists of putative orthologous genes, together with numerous analytical tools and links to existing online resources. The data are stored in a relational database, accessible by a number of user-friendly search methods and graphical browsers. The database schema is generic and can easily be applied to other bacterial genomes. Two such databases, CampyDB (for the analysis of Campylobacter spp.) and ClostriDB (for Clostridium spp.) are also available at http://campy.bham.ac.uk and http://clostri. bham.ac.uk, respectively. An example of the power of E.coli comparative analyses such as those available through coliBASE is presented.

Computational Biology↗

PubMed2000

Fast quantum search algorithms in protein sequence comparisons: quantum bioinformatics.

Quantum search algorithms are considered in the context of protein sequence comparison in bioinformatics. Given a sample protein sequence of length m (i.e., m residues), the problem considered is to find an optimal match in a large database containing N residues. Initially, Grover's quantum search algorithm is applied to a simple illustrative case-namely, where the database forms a complete set of states over the 2(m) basis states of a m qubit register, and thus is known to contain the exact sequence of interest. This example demonstrates explicitly the typical O(square root of [N]) speedup on the classical O(N) requirements. An algorithm is then presented for the (more realistic) case where the database may contain repeat sequences, and may not necessarily contain an exact match to the sample sequence. In terms of minimizing the Hamming distance between the sample sequence and the database subsequences the algorithm finds an optimal alignment, in O(square root of [N]) steps, by employing an extension of Grover's algorithm, due to Boyer et al. for the case when the number of matches is not a priori known.

Algorithms↗

PubMed1999

Use of BONSAI decision trees for the identification of potential MHC class I peptide epitope motifs.

Recognition of short peptides of 8 to 10 mer bound to MHC class I molecules by cytotoxic T lymphocytes forms the basis of cellular immunity. While the sequence motifs necessary for binding of intracellular peptides to MHC have been well studied, little is known about sequence motifs that may cause preferential affinity to the T cell receptor and/or preferential recognition and response by T cells. Here we demonstrate that computational learning systems can be useful to elucidate sequence motifs that affect T cell activation. Knowledge of T cell activation motifs could be useful for targeted vaccine design or immunotherapy. With the BONSAI computational learning algorithm, using a database of previously reported MHC bound peptides that had positive or negative T cell responses, we were able to identify sequence motif rules that explain 70% of positive T cell responses and 84% of negative T cell responses.

Algorithms↗