Oomycetes Transcriptomics Database

 


Welcome to the OTD 4.0

Phytophthora image

Oomycetes, Soybean Transcripts

Oomycetes Transcriptomics Database is an integrated transcriptome and EST data resource for oomycete pathogens. The database currently stores processed ABI SOLiD transcript sequences from Phytophthora sojae mycelial and plant infection libraries as well as Illumina transcript sequences from five Hyaloperonospora arabidopsidis libraries. In addition to those resources, it has also a complete set of Sanger EST sequences from P. sojae, P. infestans and H. arabidopsidis grown under various conditions. A new web-based transcriptome browser was created for visualization of assembled transcripts, their mapping to the reference genome, expression profiling and depth of read coverage for a particular location on the genome. The transcriptome browser merges EST derived contigs with NGS derived assembled transcripts on the fly and displays the consensus. OTD possesses strong query features and the database interacts with VBI Microbial Database as well as the Phytophthora Transcriptomics Database. The legacy EST data of P.sojae comes from 10 libraries e.g; sHA,sHB,sMA,sML,sMY,sMC,sZG,sZO,sZS,iMY with a total of 33350 raw sequences. Additionally, there are 99,320 EST sequences from P.infestans from NCBI. For P.infestans sequences cleaning information is not available. These sequences are clustered and assembled and data analysis was performed by us. We have separated Soybean ESTs from P.sojae libraries using insillico methods. The soybean libraries are named as gHA and gHB based on their origin from sHA or sHB.

All publicly avaialble soybean unigenes(37,465) are added to this database. For public soybean sequences we did not perform any cleaning or assembly. The unigenes were annotated prior to storing. Recently, we added 37492 ESTs from Hyaloperonospora arabidopsidis. All the ESTs are clustered into unigenes and annotated using blastx to nr database, interproscan, TMHMM, TargetP and SignalP. Annotations are updated every 3 months.




Oomycetes Transcriptomics Database Version 4.0 maintained at VBI 2004-2012; at CSIR-IICB from 2013 onwards in collaboration with Oregon State University For comments and suggestions email: Site Admin