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This article is part of the supplement: Eighth International Conference on Bioinformatics (InCoB2009): Computational Biology

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MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads

Hua Bao1, Yuanyan Xiong1, Hui Guo1, Renchao Zhou1, Xuemei Lu1, Zhen Yang2, Yang Zhong2 and Suhua Shi1*

Author affiliations

1 State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China

2 School of Life Sciences, Fudan University, Shanghai, 200433, PR China

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Citation and License

BMC Genomics 2009, 10(Suppl 3):S13  doi:10.1186/1471-2164-10-S3-S13

Published: 3 December 2009



Next-generation sequencing technologies provide exciting avenues for studies of transcriptomics and population genomics. There is an increasing need to conduct spliced and unspliced alignments of short transcript reads onto a reference genome and estimate minor allele frequency from sequences of population samples.


We have designed and implemented MapNext, a software tool for both spliced and unspliced alignments of short sequence reads onto reference sequences, and automated SNP detection using neighbourhood quality standards. MapNext provides four main analyses: (i) unspliced alignment and clustering of reads, (ii) spliced alignment of transcript reads over intron boundaries, (iii) SNP detection and estimation of minor allele frequency from population sequences, and (iv) storage of result data in a database to make it available for more flexible queries and for further analyses. The software tool has been tested using both simulated and real data.


MapNext is a comprehensive and powerful tool for both spliced and unspliced alignments of short reads and automated SNP detection from population sequences. The simplicity, flexibility and efficiency of MapNext makes it a valuable tool for transcriptomic and population genomic research.