2008

  • [DOI] T. Rausch, A. Emde, D. Weese, A. Döring, C. Notredame, and K. Reinert, “Segment-based multiple sequence alignment.,” Bioinformatics (oxford, england), vol. 24, iss. 16, p. i187–192, 2008.
    [Bibtex]
    @article{Rausch:2008bk,
    author = {Rausch, T and Emde, A and Weese, David and D{"o}ring, Andreas and Notredame, C and Reinert, Knut},
    title = {{Segment-based multiple sequence alignment.}},
    journal = {Bioinformatics (Oxford, England)},
    year = {2008},
    volume = {24},
    number = {16},
    pages = {i187--192},
    month = aug,
    affiliation = {International Max Planck Research School for Computational Biology and Scientific Computing, Ihnestr 63-73, 14195 Berlin, Germany. rausch@inf.fu-berlin.de},
    doi = {10.1093/bioinformatics/btn281},
    pmid = {18689823},
    language = {English},
    read = {Yes},
    rating = {0},
    date-added = {2008-10-31T11:26:05GMT},
    date-modified = {2016-01-14T20:15:17GMT},
    abstract = {MOTIVATION:Many multiple sequence alignment tools have been developed in the past, progressing either in speed or alignment accuracy. Given the importance and wide-spread use of alignment tools, progress in both categories is a contribution to the community and has driven research in the field so far.
    RESULTS:We introduce a graph-based extension to the consistency-based, progressive alignment strategy. We apply the consistency notion to segments instead of single characters. The main problem we solve in this context is to define segments of the sequences in such a way that a graph-based alignment is possible. We implemented the algorithm using the SeqAn library and report results on amino acid and DNA sequences. The benefit of our approach is threefold: (1) sequences with conserved blocks can be rapidly aligned, (2) the implementation is conceptually easy, generic and fast and (3) the consistency idea can be extended to align multiple genomic sequences.
    AVAILABILITY:The segment-based multiple sequence alignment tool can be downloaded from http://www.seqan.de/projects/msa.html. A novel version of T-Coffee interfaced with the tool is available from http://www.tcoffee.org. The usage of the tool is described in both documentations.},
    url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=18689823&retmode=ref&cmd=prlinks},
    local-url = {file://localhost/Users/reinert/Dropbox/Library.papers3/Articles/2008/Rausch/Bioinformatics%202008%20Rausch.pdf},
    file = {{Bioinformatics 2008 Rausch.pdf:/Users/reinert/Dropbox/Library.papers3/Articles/2008/Rausch/Bioinformatics 2008 Rausch.pdf:application/pdf}},
    uri = {url{papers3://publication/doi/10.1093/bioinformatics/btn281}}
    }
  • [DOI] A. Döring, D. Weese, T. Rausch, and K. Reinert, “SeqAn an efficient, generic C++ library for sequence analysis.,” Bmc bioinformatics, vol. 9, iss. 1, p. 11, 2008.
    [Bibtex]
    @article{doring_08_seqan,
    author = {D{"o}ring, Andreas and Weese, David and Rausch, T and Reinert, Knut},
    title = {{SeqAn an efficient, generic C++ library for sequence analysis.}},
    journal = {BMC Bioinformatics},
    year = {2008},
    volume = {9},
    number = {1},
    pages = {11},
    publisher = {BioMed Central Ltd},
    affiliation = {Algorithmische Bioinformatik, Institut f{"u}r Informatik, Takustr, 9, 14195 Berlin, Germany. doering@inf.fu-berlin.de},
    doi = {10.1186/1471-2105-9-11},
    pmid = {18184432},
    pmcid = {PMC2246154},
    language = {English},
    read = {Yes},
    rating = {0},
    date-added = {2009-11-24T15:28:08GMT},
    date-modified = {2016-01-14T20:15:25GMT},
    abstract = {BACKGROUND:The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome 1 would not have been possible without advanced assembly algorithms. However, owing to the high speed of technological progress and the urgent need for bioinformatics tools, there is a widening gap between state-of-the-art algorithmic techniques and the actual algorithmic components of tools that are in widespread use.
    RESULTS:To remedy this trend we propose the use of SeqAn, a library of efficient data types and algorithms for sequence analysis in computational biology. SeqAn comprises implementations of existing, practical state-of-the-art algorithmic components to provide a sound basis for algorithm testing and development. In this paper we describe the design and content of SeqAn and demonstrate its use by giving two examples. In the first example we show an application of SeqAn as an experimental platform by comparing different exact string matching algorithms. The second example is a simple version of the well-known MUMmer tool rewritten in SeqAn. Results indicate that our implementation is very efficient and versatile to use.
    CONCLUSION:We anticipate that SeqAn greatly simplifies the rapid development of new bioinformatics tools by providing a collection of readily usable, well-designed algorithmic components which are fundamental for the field of sequence analysis. This leverages not only the implementation of new algorithms, but also enables a sound analysis and comparison of existing algorithms.},
    url = {http://www.biomedcentral.com/1471-2105/9/11},
    local-url = {file://localhost/Users/reinert/Dropbox/Library.papers3/Articles/2008/oring/BMC%20Bioinformatics%202008%20oring.pdf},
    file = {{BMC Bioinformatics 2008 oring.pdf:/Users/reinert/Dropbox/Library.papers3/Articles/2008/oring/BMC Bioinformatics 2008 oring.pdf:application/pdf;BMC Bioinformatics 2008 oring.pdf:/Users/reinert/Dropbox/Library.papers3/Articles/2008/oring/BMC Bioinformatics 2008 oring.pdf:application/pdf}},
    uri = {url{papers3://publication/doi/10.1186/1471-2105-9-11}}
    }
  • T. Rausch, A. Emde, and K. Reinert, “Robust consensus computation,” Bmc bioinformatics, vol. 9, iss. Suppl 10, p. P4, 2008.
    [Bibtex]
    @article{Rausch:2008ws,
    author = {Rausch, T and Emde, A and Reinert, Knut},
    title = {{Robust consensus computation}},
    journal = {BMC Bioinformatics},
    year = {2008},
    volume = {9},
    number = {Suppl 10},
    pages = {P4},
    rating = {0},
    date-added = {2013-09-04T14:04:14GMT},
    date-modified = {2016-01-14T20:15:30GMT},
    abstract = { BMC Bioinformatics Open Access Poster presentation computation Tobias * 1,2 , Anne-Katrin Emde 1,2 and Knut 2 },
    url = {http://www.biomedcentral.com/content/pdf/1471-2105-9-s10-p4.pdf},
    local-url = {file://localhost/Users/reinert/Dropbox/Library.papers3/Articles/2008/Rausch/BMC%20Bioinformatics%202008%20Rausch.pdf},
    file = {{BMC Bioinformatics 2008 Rausch.pdf:/Users/reinert/Dropbox/Library.papers3/Articles/2008/Rausch/BMC Bioinformatics 2008 Rausch.pdf:application/pdf}},
    uri = {url{papers3://publication/uuid/BE347016-88AA-4642-81DC-E1EE604F9E2E}}
    }
2016-02-16T11:00:56+00:00