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Citations per year

Number of citations per year for the bioinformatics software tool fragrep

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fragrep specifications


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




No version available



  • person_outline Axel Mosig
  • person_outline Axel Mosig

Additional information

Publication for fragrep

fragrep citations


The functional requirement of two structural domains within telomerase RNA emerged early in eukaryotes

Nucleic Acids Res
PMCID: 5175330
PMID: 27378779
DOI: 10.1093/nar/gkw605

[…] ition to the four recently identified trypanosome TR species, we identified a TR homolog from the draft genome of the African crocodilian trypanosome T. grayi (). T. grayi TR was identified using the Fragrep2 program () and a position weight matrix derived from the sequence alignment of the four known trypanosome TR species (see Materials and Methods). This putative TR from T. grayi is seemingly a […]


The common ancestral core of vertebrate and fungal telomerase RNAs

Nucleic Acids Res
PMCID: 3592445
PMID: 23093598
DOI: 10.1093/nar/gks980

[…] R) 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 () for […]


U7 snRNAs: A Computational Survey

PMCID: 5054213
PMID: 18267300
DOI: 10.1016/S1672-0229(08)60006-6

[…] ttern in indicates quite clearly that such methods are bound to fail outside the four groups with experimentally known sequences (tetrapods, teleosts, sea urchins, and flies). Indeed, both BLAST and Fragrep did not provide additional candidates that could be unambiguously classified as U7 snRNAs based on sequence information alone.The comparison of the U7 hairpins in the different clades () reve […]

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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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