SpliceMap

Application data
Created by	Kin Fai Au, John Mu
Biological application domain(s)	RNA-Seq Alignment
Principal bioinformatics method(s)	Mapping
Created at	Stanford University
Maintained?	Yes
Output format(s)	SAM
Programming language(s)	Python, C++
Operating system(s)	Linux

Summary: Detects splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to improve mapping accuracy.

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Limitations

• Minimum read length is 50bp
• No color space support

Links

• SpliceMap Homepage [ edit link ]

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References

1. . 2010. Nucleic Acids Research

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