Segemehl statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Segemehl

Tool usage distribution map

This map represents all the scientific publications referring to Segemehl per scientific context
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Associated diseases

This word cloud represents Segemehl usage per disease context

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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




No version available


  • person_outline Steve Hoffmann

Publications for Segemehl

Segemehl citations


Discovery of physiological and cancer related regulators of 3′ UTR processing with KAPAC

Genome Biol
PMCID: 5875010
PMID: 29592812
DOI: 10.1186/s13059-018-1415-3

[…] l and si-PCPB1-treated cells were downloaded from SRA (accession SRP022151) and converted to fastq format. Reverse complemented and duplicate-collapsed reads were then mapped to the human genome with segemehl version 0.1.7 []. We did not use STAR for these data sets because these libraries, generated by DRS (direct RNA sequencing) had a high fraction of short reads that STAR did not map. From uniq […]


Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella

Proc Natl Acad Sci U S A
PMCID: 5856525
PMID: 29487214
DOI: 10.1073/pnas.1714718115

[…] form was carried out by Vertis Biotechnologie, Germany. All protocols were identical to those used previously (, ). Sequence reads were mapped against the S. Typhimurium D23580 reference genome using Segemehl, with accuracy set to 100% (, ). RNA-seq and dRNA-seq data can be downloaded as raw reads (.fastq file format); the Gene Expression Omnibus database accession no. is GSE108104. […]


Whole genome sequencing of Leptospira interrogans from southern Brazil: genetic features of a highly virulent strain

PMCID: 5722262
PMID: 29236923
DOI: 10.1590/0074-02760170130

[…] h as single-nucleotide polymorphisms (SNPs), a variant calling analysis was performed. The filtered sequencing reads were aligned to the reference genome of L. interrogans strain Fiocruz L1-130 using Segemehl ( and an initial identification of INDELs was performed using SAMtools and BCFtools (, which were processed loca […]


A Dipteran’s Novel Sucker Punch: Evolution of Arthropod Atypical Venom with a Neurotoxic Component in Robber Flies (Asilidae, Diptera)

PMCID: 5793116
PMID: 29303983
DOI: 10.3390/toxins10010029

[…] nd the effective length of a transcript into account. Is it important to note, that Kallisto uses an approximation of effective length of every transcript for the calculation of the TPM, while in the Segemehl approach the complete length of the coding region is used for length normalization. To minimize the false positive aligned reads, the bootstrap value was set to 100. […]


Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq dependent translational regulation in Pseudomonas aeruginosa

Nucleic Acids Res
PMCID: 5815094
PMID: 29244160
DOI: 10.1093/nar/gkx1245
call_split See protocol

[…] lity ( Sequencing adapter removal was performed with cutadapt (). Mapping of the samples against the PAO1 reference genome (NCBI accession number NC_002516.2) was performed with Segemehl () with default parameters. Reads mapping to regions annotated as either rRNA or tRNA were discarded from all data and ignored for all follow up analysis steps. The mapped sequencing data wer […]


Evaluating the bias of circRNA predictions from total RNA Seq data

PMCID: 5762294
PMID: 29340026
DOI: 10.18632/oncotarget.22972

[…] hed circRNA prediction algorithms CIRI (CIRI1.2 and CIRI2.0) and KNIFE to predict novel circRNAs from total RNA-Seq data, since CIRI algorithm have showed the advantage over the other two algorithms, segemehl and find_circ []. As for KNIFE algorithm, unlike previous algorithms that were lack of rigorous statistical testing, it used a statistical approach to decrease false positive identification [ […]

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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.