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FANSe2 specifications

Information


Unique identifier OMICS_31342
Name FANSe2
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Windows
Parallelization MPI
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Gong Zhang
  • person_outline Qing-Yu He

Publication for FANSe2

FANSe2 citations

 (6)
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CD215+ Myeloid Cells Respond to Interleukin 15 Stimulation and Promote Tumor Progression

2017
Front Immunol
PMCID: 5722806
PMID: 29255466
DOI: 10.3389/fimmu.2017.01713
call_split See protocol

[…] were mapped to the mouse RefSeq-RNA reference sequence (downloaded from http://hgdownload.cse.ucsc.edu/downloads) using the FANSe 2 algorithm (available from http://bioinformatics.jnu.edu.cn/software/fanse2/) with the parameters −L85 −E3 −U0 −S1015. Alternative splice variants were merged. Genes with at least 10 mapped reads were considered to be reliably detected genes. These genes were further q […]

call_split

In vitro biomimetic platforms featuring a perfusion system and 3D spheroid culture promote the construction of tissue engineered corneal endothelial layers

2017
Sci Rep
PMCID: 5429708
PMID: 28396609
DOI: 10.1038/s41598-017-00914-1
call_split See protocol

[…] he number of reads per kilobase of exon model per million mapped reads (FPKM) to obtain normalized gene expression levels. We mapped the original RNA-seq to the reference transcriptome sequence using FANSe2 as previously described. The correlation coefficients between gene expression levels were calculated and plotted as a correlation heatmap. Gene ontology (GO) analysis was performed using TopGO […]

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Rpph1 Upregulates CDC42 Expression and Promotes Hippocampal Neuron Dendritic Spine Formation by Competing with miR 330 5p

2017
PMCID: 5293807
PMID: 28223918
DOI: 10.3389/fnmol.2017.00027
call_split See protocol

[…] 2 N (ambiguous nucleotides) were retained. Moreover, paired reads that mapped to the SILVA database were discarded. The cleaned reads of each sample were aligned to the mouse RNA Ensembl database by FANSe2, allowing 7 nucleotide mismatches. All unigene clusters with at least 10 mapped reads were considered as reliable transcripts. To analyze differentially expressed unigenes, the expression of ea […]

call_split

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

2016
PLoS Genet
PMCID: 4771717
PMID: 26926465
DOI: 10.1371/journal.pgen.1005901
call_split See protocol

[…] , 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 #x2013;L55 –E4 –U0 –S10. Alternative splice variants were merged []. The expression levels were estimated by using the rpkM unit []. The mRNA length information wa […]

library_books

Transcriptome Analysis of the SL221 Cells at the Early Stage during Spodoptera litura Nucleopolyhedrovirus Infection

2016
PLoS One
PMCID: 4739724
PMID: 26840182
DOI: 10.1371/journal.pone.0147873

[…] mples were cleaned by removing redundancies and were further assembled as all-unigenes using CD-HIT software []. The cleaned reads were strand-specifically aligned to the assembled all-unigenes using FANSe2 allowing 7 nt of mismatch [,]. The all-unigenes with at least 10 mapped reads were considered reliably assembled unigenes.The COG and KEGG pathway annotations were performed via blastx search a […]

library_books

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

2015
Sci Rep
PMCID: 4607945
PMID: 26472343
DOI: 10.1038/srep15407

[…] rs in these contigs. Therefore, it is essential to employ de novo transcriptome assembly algorithms such as Trinity, and mapping algorithms with high error-tolerance, accuracy, and robustness such as FANSe2 to efficiently map the reads to the assembled contigs and to identify DEGs, as shown in this study. Less robust and less accurate algorithms, such as Bowtie, fail to map most of the reads to th […]

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FANSe2 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
FANSe2 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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