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  • 1
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2007
    In:  BMC Bioinformatics Vol. 8, No. 1 ( 2007-12)
    In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2007-12)
    Abstract: Whole genome shotgun sequencing produces increasingly higher coverage of a genome with random sequence reads. Progressive whole genome assembly and eventual finishing sequencing is a process that typically takes several years for large eukaryotic genomes. In the interim, all sequence reads of public sequencing projects are made available in repositories such as the NCBI Trace Archive. For a particular locus, sequencing coverage may be high enough early on to produce a reliable local genome assembly. We have developed software, Tracembler , that facilitates in silico chromosome walking by recursively assembling reads of a selected species from the NCBI Trace Archive starting with reads that significantly match sequence seeds supplied by the user. Results Tracembler takes one or multiple DNA or protein sequence(s) as input to the NCBI Trace Archive BLAST engine to identify matching sequence reads from a species of interest. The BLAST searches are carried out recursively such that BLAST matching sequences identified in previous rounds of searches are used as new queries in subsequent rounds of BLAST searches. The recursive BLAST search stops when either no more new matching sequences are found, a given maximal number of queries is exhausted, or a specified maximum number of rounds of recursion is reached. All the BLAST matching sequences are then assembled into contigs based on significant sequence overlaps using the CAP3 program. We demonstrate the validity of the concept and software implementation with an example of successfully recovering a full-length Chrm2 gene as well as its upstream and downstream genomic regions from Rattus norvegicus reads. In a second example, a query with two adjacent Medicago truncatula genes as seeds resulted in a contig that likely identifies the microsyntenic homologous soybean locus. Conclusion Tracembler streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads. A web server hosting Tracembler is provided at http://www.plantgdb.org/tool/tracembler/ , and the software is also freely available from the authors for local installations.
    Type of Medium: Online Resource
    ISSN: 1471-2105
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2007
    detail.hit.zdb_id: 2041484-5
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Elsevier BV ; 2008
    In:  Computer Networks Vol. 52, No. 9 ( 2008-6), p. 1782-1796
    In: Computer Networks, Elsevier BV, Vol. 52, No. 9 ( 2008-6), p. 1782-1796
    Type of Medium: Online Resource
    ISSN: 1389-1286
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2008
    detail.hit.zdb_id: 1499744-7
    detail.hit.zdb_id: 224452-4
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  • 3
    Online Resource
    Online Resource
    Biomedical Informatics ; 2009
    In:  Bioinformation Vol. 3, No. 7 ( 2009-02-26), p. 296-298
    In: Bioinformation, Biomedical Informatics, Vol. 3, No. 7 ( 2009-02-26), p. 296-298
    Type of Medium: Online Resource
    ISSN: 0973-8894 , 0973-2063
    URL: Issue
    Language: Unknown
    Publisher: Biomedical Informatics
    Publication Date: 2009
    detail.hit.zdb_id: 2203786-X
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  • 4
    Online Resource
    Online Resource
    Association for Computing Machinery (ACM) ; 2006
    In:  ACM SIGMETRICS Performance Evaluation Review Vol. 34, No. 1 ( 2006-06-26), p. 311-322
    In: ACM SIGMETRICS Performance Evaluation Review, Association for Computing Machinery (ACM), Vol. 34, No. 1 ( 2006-06-26), p. 311-322
    Abstract: Serving as the core component in many packet forwarding, differentiating and filtering schemes, packet classification continues to grow its importance in today's IP networks. Currently, most vendors use Ternary CAMs (TCAMs) for packet classification. TCAMs usually use brute-force parallel hardware to simultaneously check for all rules. One of the fundamental problems of TCAMs is that TCAMs suffer from range specifications because rules with range specifications need to be translated into multiple TCAM entries. Hence, the cost of packet classification will increase substantially as the number of TCAM entries grows. As a result, network operators hesitate to configure packet classifiers using range specifications. In this paper, we optimize packet classifier configurations by identifying semantically equivalent rule sets that lead to reduced number of TCAM entries when represented in hardware. In particular, we develop a number of effective techniques, which include: trimming rules, expanding rules, merging rules, and adding rules. Compared with previously proposed techniques which typically require modifications to the packet processor hardware, our scheme does not require any hardware modification, which is highly preferred by ISPs. Moreover, our scheme is complementary to previous techniques in that those techniques can be applied on the rule sets optimized by our scheme. We evaluate the effectiveness and potential of the proposed techniques using extensive experiments based on both real packet classifiers managed by a large tier-1 ISP and synthetic data generated randomly. We observe significant reduction on the number of TCAM entries that are needed to represent the optimized packet classifier configurations.
    Type of Medium: Online Resource
    ISSN: 0163-5999
    Language: English
    Publisher: Association for Computing Machinery (ACM)
    Publication Date: 2006
    detail.hit.zdb_id: 199353-7
    detail.hit.zdb_id: 2089001-1
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  • 5
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2009
    In:  BMC Genomics Vol. 10, No. 1 ( 2009-12)
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 10, No. 1 ( 2009-12)
    Abstract: EST sequencing projects are increasing in scale and scope as the genome sequencing technologies migrate from core sequencing centers to individual research laboratories. Effectively, generating EST data is no longer a bottleneck for investigators. However, processing large amounts of EST data remains a non-trivial challenge for many. Web-based EST analysis tools are proving to be the most convenient option for biologists when performing their analysis, so these tools must continuously improve on their utility to keep in step with the growing needs of research communities. We have developed a web-based EST analysis pipeline called ESTPiper, which streamlines typical large-scale EST analysis components. Results The intuitive web interface guides users through each step of base calling, data cleaning, assembly, genome alignment, annotation, analysis of gene ontology (GO), and microarray oligonucleotide probe design. Each step is modularized. Therefore, a user can execute them separately or together in batch mode. In addition, the user has control over the parameters used by the underlying programs. Extensive documentation of ESTPiper's functionality is embedded throughout the web site to facilitate understanding of the required input and interpretation of the computational results. The user can also download intermediate results and port files to separate programs for further analysis. In addition, our server provides a time-stamped description of the run history for reproducibility. The pipeline can also be installed locally, allowing researchers to modify ESTPiper to suit their own needs. Conclusion ESTPiper streamlines the typical process of EST analysis. The pipeline was initially designed in part to support the Daphnia pulex cDNA sequencing project. A web server hosting ESTPiper is provided at http://estpiper.cgb.indiana.edu/ to now support projects of all size. The software is also freely available from the authors for local installations.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2009
    detail.hit.zdb_id: 2041499-7
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Association for Computing Machinery (ACM) ; 2007
    In:  ACM SIGMETRICS Performance Evaluation Review Vol. 35, No. 1 ( 2007-06-12), p. 253-264
    In: ACM SIGMETRICS Performance Evaluation Review, Association for Computing Machinery (ACM), Vol. 35, No. 1 ( 2007-06-12), p. 253-264
    Abstract: Packet classification is the foundation of many Internet functions such as QoS and security. A long thread of research has proposed efficient software-based solutions to this problem. Such software solutions are attractive because they require cheap memory systems for implementation, thus bringing down the overall cost of the system. In contrast, hardware-based solutions use more expensive memory systems, e.g., TCAMs, but are often preferred by router vendors for their faster classification speeds. The goal of this paper is to find a "best-of-both-worlds" solution -- a solution that incurs the cost of a software-based system and has the speed of a hardware-based one. Our proposed solution, called smart rule cache achieves this goal by using minimal hardware -- a few additional registers -- to cache evolving rules which preserve classification semantics, and additional logic to match incoming packets to these rules. Using real traffic traces and real rule sets from a tier-1 ISP, we show such a setup is sufficient to achieve very high hit ratios for fast classification in hardware. Cache miss ratios are 2 ∼ 4 orders of magnitude lower than flow cache schemes. Given its low cost and good performance, we believe our solution may create significant impact on current industry practice.
    Type of Medium: Online Resource
    ISSN: 0163-5999
    Language: English
    Publisher: Association for Computing Machinery (ACM)
    Publication Date: 2007
    detail.hit.zdb_id: 199353-7
    detail.hit.zdb_id: 2089001-1
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  • 7
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2009
    In:  Bioinformatics Vol. 25, No. 7 ( 2009-04-01), p. 956-957
    In: Bioinformatics, Oxford University Press (OUP), Vol. 25, No. 7 ( 2009-04-01), p. 956-957
    Abstract: Summary: Investigating the conservation of gene clusters across multiple genomes has become a standard practice in the era of comparative genomics. However, all existing software and databases rely heavily on pre-computation to identify homologous genes by genome-wide comparisons. Such pre-computing strategies lack accuracy and updating the data is computationally intensive. Since most molecular biologists are often interested only in a small cluster of genes, catering to this need, we have developed a web-based software system that allows users to upload a list of genes, perform dynamic search against the genomes of their choices and interactively visualize the gene cluster conservation using a novel multi-genome browser. Our approach avoids expensive genome-wide pre-computing and allows users to dynamically change the search criteria to fit their genes of interest. Our system can be customized for any genome sequences. We have applied it to both prokaryotic and eukaryotic genomes to illustrate its usability. Availability: Our software is freely available at http://cgcv.cgb.indiana.edu/cgi-bin/index.cgi. Contact:  dongq@indiana.edu
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2009
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2009
    In:  Bioinformatics Vol. 25, No. 12 ( 2009-06-15), p. 1550-1551
    In: Bioinformatics, Oxford University Press (OUP), Vol. 25, No. 12 ( 2009-06-15), p. 1550-1551
    Abstract: Summary: The Generic Genome Browser (GBrowse) is one of the most widely used tools for visualizing genomic features along a reference sequence. However, the installation and configuration of GBrowse is not trivial for biologists. We have developed a web server, WebGBrowse that allows users to upload genome annotation in the GFF3 format, configure the display of each genomic feature by simply using a web browser and visualize the configured genomic features with the integrated GBrowse software. Availability: WebGBrowse is accessible via http://webgbrowse.cgb.indiana.edu/ and the system is also freely available for local installations. Contact:  dongq@indiana.edu
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2009
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2008
    In:  BMC Genomics Vol. 9, No. 1 ( 2008-12)
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2008-12)
    Abstract: The BLAST program is one of the most widely used sequence similarity search tools for genomic research, even by those biologists lacking extensive bioinformatics training. As the availability of sequence data increases, more researchers are downloading the BLAST program for local installation and performing larger and more complex tasks, including batch queries. In order to manage and interpret the results of batch queries, a host of software packages have been developed to assist with data management and post-processing. Among these programs, there is almost a complete lack of visualization tools to provide graphic representation of complex BLAST pair-wise alignments. We have developed a web-based program, B LAST O utput V isualization Tool (BOV), that allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns. Results Users can upload the standard BLAST output in pair-wise alignment format as input to the web server (including batch queries generated installing and running the stand-alone BLAST program on a local server). The program extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence. The coordinates are used to plot each matching region as colored lines or trapezoids. Using the straightforward control panels throughout the web site, each plotted matching region can be easily explored in detail by, for example, highlighting the region of interest or examining the raw pair-wise sequence alignment. Tutorials are provided at the website to guide users step-by-step through the functional features of BOV. Conclusion BOV provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets. In particular, this software is valuable to users interested in identifying regions of co-linearity, duplication, translocation, and inversion among sequences. A web server hosting BOV is accessible via http://bioportal.cgb.indiana.edu/cgi-bin/BOV/index.cgi and the software is freely available for local installations.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2008
    detail.hit.zdb_id: 2041499-7
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2005
    In:  Plant Physiology Vol. 139, No. 2 ( 2005-10-01), p. 610-618
    In: Plant Physiology, Oxford University Press (OUP), Vol. 139, No. 2 ( 2005-10-01), p. 610-618
    Abstract: PlantGDB (http://www.plantgdb.org/) is a database of plant molecular sequences. Expressed sequence tag (EST) sequences are assembled into contigs that represent tentative unique genes. EST contigs are functionally annotated with information derived from known protein sequences that are highly similar to the putative translation products. Tentative Gene Ontology terms are assigned to match those of the similar sequences identified. Genome survey sequences are assembled similarly. The resulting genome survey sequence contigs are matched to ESTs and conserved protein homologs to identify putative full-length open reading frame-containing genes, which are subsequently provisionally classified according to established gene family designations. For Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the exon-intron boundaries for gene structures are annotated by spliced alignment of ESTs and full-length cDNAs to their respective complete genome sequences. Unique genome browsers have been developed to present all available EST and cDNA evidence for current transcript models (for Arabidopsis, see the AtGDB site at http://www.plantgdb.org/AtGDB/; for rice, see the OsGDB site at http://www.plantgdb.org/OsGDB/). In addition, a number of bioinformatic tools have been integrated at PlantGDB that enable researchers to carry out sequence analyses on-site using both their own data and data residing within the database.
    Type of Medium: Online Resource
    ISSN: 1532-2548 , 0032-0889
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2005
    detail.hit.zdb_id: 2004346-6
    detail.hit.zdb_id: 208914-2
    SSG: 12
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