fragrep statistics

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Associated diseases

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fragrep specifications

Information


Unique identifier OMICS_29782
Name fragrep
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 2
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Axel Mosig <>
  • person_outline Axel Mosig <>

Additional information


http://www.bioinf.uni-leipzig.de/Software/fragrep/fragrep-tutorial.html

Publication for fragrep

fragrep in publications

 (2)
PMCID: 5175330
PMID: 27378779
DOI: 10.1093/nar/gkw605

[…] limited to watson–crick base-pairs and g:u pairings were treated as neutral variations., each strand of the draft genome of trypanosoma grayi () was analyzed with a search pattern generated in the fragrep2 program () from the multiple sequence alignment of the four trypanosome trs annotated for regions of high conservation. the single hit for the t. grayi tr sequence was obtained from the t. […]

PMCID: 3592445
PMID: 23093598
DOI: 10.1093/nar/gks980

[…] was identified by searching for putative template and sequences conserved in the 73 filamentous ascomycete ters. first, putative template sequences were identified in the s. complicata genome with fragrep (). for each occurrence, an additional 1-kb sequence upstream and 3-kb sequence downstream of the putative template were extracted. these 4-kb spans were then searched with infernal 1.0 () […]


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fragrep institution(s)
Department of Combinatorics and Geometry, CAS/MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria; The Santa Fe Institute, Santa Fe, NM, USA; Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
fragrep funding source(s)
Supported by the Bioinformatics Initiative (BIZ-6/1-2) of the German Research Association (DFG).

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