peanutdb an integrated bioinformatics web portal for arachis hypogaea transcriptomicspeanutdb综合生物信息学门户网站对落花生hypogaea转录组.pdfVIP

Duan et al. BMC Plant Biology 2012, 12:94 /1471-2229/12/94 DATABASE Open Access PeanutDB: an integrated bioinformatics web portal for Arachis hypogaea transcriptomics 1 2,3 2 2,3 2 1 1* Xiaohong Duan , Emily Schmidt , Pei Li , Douglas Lenox , Lin Liu , Changlong Shu , Jie Zhang and Chun Liang2,3* Abstract Background: The peanut (Arachis hypogaea) is an important crop cultivated worldwide for oil production and food sources. Its complex genetic architecture (e.g., the large and tetraploid genome possibly due to unique cross of wild diploid relatives and subsequent chromosome duplication: 2n = 4x = 40, AABB, 2800 Mb) presents a major challenge for its genome sequencing and makes it a less-studied crop. Without a doubt, transcriptome sequencing is the most effective way to harness the genome structure and gene expression dynamics of this non-model species that has a limited genomic resource. Description: With the development of next generation sequencing technologies such as 454 pyro-sequencing and Illumina sequencing by synthesis, the transcriptomics data of peanut is rapidly accumulated in both the public databases and private sectors. Integrating 187,636 Sanger reads (103,685,419 bases), 1,165,168 Roche 454 reads (333,862,593 bases) and 57,135,995 Illumina reads (4,073,740,115 bases), we generated the first release of our peanut transcriptome assembly that contains 32,619 contigs. We provided EC, KEGG and GO functional annotations to these contigs and detected SSRs, SNPs and other genetic polymorphisms for each contig. Based on both open-source and our in-house tools, PeanutDB presents many seamlessly integrated web interfaces that allow users to search, filter, navigate and visua