• [DOI] A. Emde, M. Grunert, D. Weese, K. Reinert, and S. R. Sperling, “MicroRazerS: rapid alignment of small RNA reads.,” Bioinformatics (oxford, england), vol. 26, iss. 1, p. 123–124, 2010.
    author = {Emde, A and Grunert, Marcel and Weese, David and Reinert, Knut and Sperling, Silke R},
    title = {{MicroRazerS: rapid alignment of small RNA reads.}},
    journal = {Bioinformatics (Oxford, England)},
    year = {2010},
    volume = {26},
    number = {1},
    pages = {123--124},
    month = jan,
    affiliation = {Department of Computer Science, Free University of Berlin, Takustr. 9, Berlin, Germany. emde@inf.fu-berlin.de},
    doi = {10.1093/bioinformatics/btp601},
    pmid = {19880369},
    language = {English},
    read = {Yes},
    rating = {0},
    date-added = {2010-03-24T08:35:42GMT},
    date-modified = {2016-01-14T20:14:26GMT},
    abstract = {MOTIVATION:Deep sequencing has become the method of choice for determining the small RNA content of a cell. Mapping the sequenced reads onto their reference genome serves as the basis for all further analyses, namely for identification and quantification. A method frequently used is Mega BLAST followed by several filtering steps, even though it is slow and inefficient for this task. Also, none of the currently available short read aligners has established itself for the particular task of small RNA mapping.
    RESULTS:We present MicroRazerS, a tool optimized for mapping small RNAs onto a reference genome. It is an order of magnitude faster than Mega BLAST and comparable in speed with other short read mapping tools. In addition, it is more sensitive and easy to handle and adjust.
    AVAILABILITY:MicroRazerS is part of the SeqAn C++ library and can be downloaded from http://www.seqan.de/projects/MicroRazerS.html.},
    url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=19880369&retmode=ref&cmd=prlinks},
    local-url = {file://localhost/Users/reinert/Dropbox/Library.papers3/Articles/2010/Emde/Bioinformatics%202010%20Emde.pdf},
    file = {{Bioinformatics 2010 Emde.pdf:/Users/reinert/Dropbox/Library.papers3/Articles/2010/Emde/Bioinformatics 2010 Emde.pdf:application/pdf}},
    uri = {\url{papers3://publication/doi/10.1093/bioinformatics/btp601}}
  • [DOI] D. Hüser, A. Gogol-Döring, T. Lutter, S. Weger, K. Winter, E. Hammer, T. Cathomen, K. Reinert, and R. Heilbronn, “Integration preferences of wildtype AAV-2 for consensus rep-binding sites at numerous loci in the human genome.,” Plos pathogens, vol. 6, iss. 7, p. e1000985, 2010.
    author = {H{\"u}ser, Daniela and Gogol-D{\"o}ring, Andreas and Lutter, Timo and Weger, Stefan and Winter, Kerstin and Hammer, Eva-Maria and Cathomen, Toni and Reinert, Knut and Heilbronn, Regine},
    title = {{Integration preferences of wildtype AAV-2 for consensus rep-binding sites at numerous loci in the human genome.}},
    journal = {PLoS Pathogens},
    year = {2010},
    volume = {6},
    number = {7},
    pages = {e1000985},
    affiliation = {Institute of Virology, Campus Benjamin Franklin, Charit{\'e}-Universit{\"a}tsmedizin Berlin, Berlin, Germany.},
    doi = {10.1371/journal.ppat.1000985},
    pmid = {20628575},
    pmcid = {PMC2900306},
    language = {English},
    read = {Yes},
    rating = {0},
    date-added = {2010-11-22T20:41:42GMT},
    date-modified = {2016-01-14T20:14:31GMT},
    abstract = {Adeno-associated virus type 2 (AAV) is known to establish latency by preferential integration in human chromosome 19q13.42. The AAV non-structural protein Rep appears to target a site called AAVS1 by simultaneously binding to Rep-binding sites (RBS) present on the AAV genome and within AAVS1. In the absence of Rep, as is the case with AAV vectors, chromosomal integration is rare and random. For a genome-wide survey of wildtype AAV integration a linker-selection-mediated (LSM)-PCR strategy was designed to retrieve AAV-chromosomal junctions. DNA sequence determination revealed wildtype AAV integration sites scattered over the entire human genome. The bioinformatic analysis of these integration sites compared to those of rep-deficient AAV vectors revealed a highly significant overrepresentation of integration events near to consensus RBS. Integration hotspots included AAVS1 with 10% of total events. Novel hotspots near consensus RBS were identified on chromosome 5p13.3 denoted AAVS2 and on chromsome 3p24.3 denoted AAVS3. AAVS2 displayed seven independent junctions clustered within only 14 bp of a consensus RBS which proved to bind Rep in vitro similar to the RBS in AAVS3. Expression of Rep in the presence of rep-deficient AAV vectors shifted targeting preferences from random integration back to the neighbourhood of consensus RBS at hotspots and numerous additional sites in the human genome. In summary, targeted AAV integration is not as specific for AAVS1 as previously assumed. Rather, Rep targets AAV to integrate into open chromatin regions in the reach of various, consensus RBS homologues in the human genome.},
    url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=20628575&retmode=ref&cmd=prlinks},
    local-url = {file://localhost/Users/reinert/Dropbox/Library.papers3/Articles/2010/H%C3%BCser/PLoS%20Pathog%202010%20H%C3%BCser.pdf},
    file = {{PLoS Pathog 2010 Hüser.pdf:/Users/reinert/Dropbox/Library.papers3/Articles/2010/Hüser/PLoS Pathog 2010 Hüser.pdf:application/pdf}},
    uri = {\url{papers3://publication/doi/10.1371/journal.ppat.1000985}}
  • A. Gogol-Döring and K. Reinert, Biological sequence analysis using the SeqAn C++ library, Crc, 2009.
    author = {Gogol-D{\"o}ring, Andreas and Reinert, Knut},
    title = {{Biological sequence analysis using the SeqAn C++ library}},
    publisher = {CRC},
    year = {2009},
    month = oct,
    isbn = {9781420076233},
    language = {English},
    rating = {0},
    date-added = {2011-06-08T20:46:19GMT},
    date-modified = {2016-01-14T20:14:34GMT},
    abstract = {A key to that invaluable resource, this book provides a highly accessible way for the rapid prototyping of algorithms in the field.},
    url = {http://books.google.com/books?hl=en&lr=&id=Qf98t1LOiBYC&oi=fnd&pg=PP1&dq=seqan+reinert&ots=4y9iyK_zEv&sig=P6EZHMUrqI1Czy6VqcwgIr4qPBg},
    uri = {\url{papers3://publication/uuid/E63A4075-298E-4848-908E-DD78EAB143E5}}