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FANSe specifications


Unique identifier OMICS_04840
Name FANSe
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability No
Maintained No


No version available


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Publication for FANSe

FANSe citations


CD215+ Myeloid Cells Respond to Interleukin 15 Stimulation and Promote Tumor Progression

Front Immunol
PMCID: 5722806
PMID: 29255466
DOI: 10.3389/fimmu.2017.01713
call_split See protocol

[…] The sequencing reads were mapped to the mouse RefSeq-RNA reference sequence (downloaded from using the FANSe 2 algorithm (available from with the parameters −L85 −E3 −U0 −S1015. Alternative splice variants were merged. Genes with at least 10 mapped rea […]


Distinct epigenomes in CD4+ T cells of newborns, middle ages and centenarians

Sci Rep
PMCID: 5137168
PMID: 27917918
DOI: 10.1038/srep38411

[…] ve reproducible genes expression profiles ().Clean sequencing reads were mapped to the human Ensembl-RNA reference sequence (downloaded from using the FANSe 2 algorithm with the parameters -L110 -E7 -U0 -S10. Alternative splice variants were merged. Genes with at least 10 mapped reads were considered to be reliably detected genes. These genes were f […]


Comparative Transcriptional Profiling of Primed and Non primed Rice Seedlings under Submergence Stress

Front Plant Sci
PMCID: 4964843
PMID: 27516766
DOI: 10.3389/fpls.2016.01125

[…] The clean sequencing reads were mapped to the rice RNA reference sequence (MSU release7, downloaded from using FANSe 2 algorithm (Zhang et al., ) with the parameters −L110 −E7 −U0 −S10. The transcripts with at least five mapped reads out of eight samples were considered as reliably detected transcripts. These […]


Correlational study on mitochondrial DNA mutations as potential risk factors in breast cancer

PMCID: 5058755
PMID: 27121313
DOI: 10.18632/oncotarget.8892

[…] Based on the Fanse 2 algorithm, we made a comparison using the Homosapiens GRCh38 genome (NC_012920) sequence as the reference and performed mutation site analysis and gene annotation. The mutation frequency was c […]


Genome Wide and Experimental Resolution of Relative Translation Elongation Speed at Individual Gene Level in Human Cells

PLoS Genet
PMCID: 4771717
PMID: 26926465
DOI: 10.1371/journal.pgen.1005901
call_split See protocol

[…] 18 nt were then discarded. The rest high quality reads were aligned to the RefSeq-RNA reference sequence (downloaded from, accessed on Jan. 21st, 2013) using FANSe 2 algorithm [] with the parameters –L60 –E2 –U1 –S10. For mRNA and RNC-mRNA sequencing datasets, the reads were mapped to RefSeq-RNA reference sequence with FANSe2 algorithm with the parameters […]


Revealing crosstalk of plant and fungi in the symbiotic roots of sewage cleaning Eichhornia crassipes using direct de novo metatranscriptomic analysis

Sci Rep
PMCID: 4607945
PMID: 26472343
DOI: 10.1038/srep15407

[…] necessitates highly accurate and error-tolerant algorithms to map the short reads onto the contigs for gene expression quantification or correction of the assembly. We have shown that highly accurate FANSe series algorithms tolerate ~20% deviation in the reference sequence, while the previous algorithm gives numerous false positives and false negatives. Therefore, our strategy may be directly empl […]


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FANSe institution(s)
Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
FANSe funding source(s)
Supported by the National ‘‘973’’ Projects of China (2011CB910700), National Natural Science Foundation of China (31300649 and 31200612), the Key Project of Chinese Ministry of Education (212207), Guangdong Natural Science Foundation (S2013010013529), Foundation for Distinguished Young Talents in Higher Education of Guangdong, China (2012LYM_0026), the Fundamental Research Funds for the Central Universities (21612202, 21612459, 11610101, 21613343 and 21611201), and the Institutional Grant of Excellence of Jinan University, China (50625072).

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