Segemehl protocols

Segemehl computational protocol

Segemehl specifications


Unique identifier OMICS_00683
Name Segemehl
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 0.3.0
Stability Stable
Maintained Yes


  • haarz



Add your version


  • person_outline Steve Hoffmann <>

Publications for Segemehl

Segemehl IN pipelines

PMCID: 5561264
PMID: 28819222
DOI: 10.1038/s41598-017-08806-0

[…] quality data were removed from the sequencing raw data using trimmomatic (version 0.32) (parameters: illuminaclip: adaptor.fa:2:30:10 leading:3 trailing:3 slidingwindow:4:15 minlen:50). the software segemehl (v 0.1.7) and ciri (v 2.0.5) were used for potential back-splice sites extraction41, 42., total rna was isolated by trizol reagent (life technologies, carlsbad, ca) followed by dna residue […]

PMCID: 5703892
PMID: 29218039
DOI: 10.3389/fmicb.2017.02312

[…] and quality trimmed with trimmomatic (bolger et al., 2014) with default parameters. mapping of the samples against the ucbpp-pa14 reference genome (accession number nc_008463) was performed with segemehl (hoffmann et al., 2009, 2014). the uniquely mapped sequencing data were split by strand and further processed for automatic ucsc genome browser visualization with the viennangs toolbox (kent […]

PMCID: 4860701
PMID: 27044515
DOI: 10.1093/gbe/evw073

[…] all reads from the eight rna-seq data sets were mapped with tophat2 (v2.0.11) (kim et al. 2013) to the human reference genome with –microexon-search. for extraction of splice sites, we used haarz (v0.1) (hoffmann et al. 2014) with default parameters. visualization of mapped reads and splice sites was performed with igv, sashimi plot (v2.0.34) (thorvaldsdóttir et al. 2012)., we examined […]

PMCID: 5001579
PMID: 26908653
DOI: 10.1093/nar/gkw115

[…] the bw2952 mc4100 reference genome and annotations (accession nc_012759) were obtained from the ncbi ftp server and reads were mapped against the reference genome with segemehl (v0.1.7) (21,22). uniquely mapped reads were extracted for the downstream analysis and processed for ucsc visualization. read count numbers for each sample were determined […]

PMCID: 5069555
PMID: 27647875
DOI: 10.15252/embj.201694857

[…] (martin, 2011). processed reads were aligned to the human transcriptome (hg38/grch38; ensembl; merged sequences from protein‐coding and non‐coding rna transcripts) (cunningham et al, 2015) using the segemehl software (hoffmann et al, 2009). the estimation of the transcript expression as well as the differential expression (de) analysis was done using the bitseq software package (glaus et al, […]

Segemehl institution(s)
Junior Research Group Transcriptome Bioinformatics, University Leipzig, Leipzig, Germany; Interdisciplinary Center for Bioinformatics and Bioinformatics Group, University Leipzig, Leipzig, Germany; LIFE Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany; Department of Theoretical Chemistry, University Vienna, Vienna, Austria; RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology – IZI, Leipzig, Germany; Max-Planck-Institute for Mathematics in the Sciences, Leipzig, Germany; Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark; Santa Fe Institute, Santa Fe, NM, USA; Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany; Department of Epidemiology and Biostatistics, Imperial College London, London, UK
Segemehl funding source(s)
Supported by LIFE (Leipzig Research Center for Civilization Diseases), Leipzig University and the Deutsche Forschungsgemeinschaft under the auspicies of SPP 1590 “Probabilistic Structures in Evolution”, proj. no. STA 850/14-1.

Segemehl review

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Rodman M X

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Quite resource demanding (time and RAM), but great tool. Especially if it comes to splice site prediction, circular RNA.