DNA database
This database will include all Physcomitrella DNA sequences deposited in public databases together with the expressed sequence tag (EST) project carried out in the National Institute for Basic Biology (NIBB) as a collaboration with the Institute of Physical and Chemical Research (RIKEN), and the National Institute of Genetics (NIG). This project was supported by the Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT) and the Japan Society for the Promotion of Science (JSPS).
All of the full-length clones established by our group are distributed from the RIKEN BioResource Center, and please send a message to plant [at] brc.riken.go.jp.
Reference: Nishiyama, T., Fujita, T., Shin-I, T., Seki, M., Nishide, H., Uchiyama, I., Kamiya, A., Carninci, P., Hayashizaki, Y., Shinozaki, K., Kohara, Y., and Hasebe, M. 2003. Comparative genomics of Physcomitrella patens gemetophytic transcriptome and Arabidopsis thaliana: Implication for land plant evolution. Proc. Natl. Acad. Sci. USA 100: 8007-8012.
How to use PHYSCObase
Services
- BLAST search against PHYSCObase
- BLAST raw WGS sequence and assemble into contigs
- Contig Pair search using Clone ID
Bulk sequence download of the Physcomitrella datasets
The following sequence datasets are available as fasta format files.
Each file is compressed with gzip.
- Windows Users: Right-Click and choose "Save file as..."
- MacOS Users: Click-hold and choose "Download file..."
- moss.seq
- Individual ESTs sequence and mRNA sequences from GenBank.
- contigs
- Contig sequences of the Physcomitrella mRNA sequences. This dataset was constructed from the moss.seq and CAP3 sequence assembly program
- pairseq
- Concatenated sequences of every putative transcripts.
- gbcontigs
- Contig sequences that are not included in pairseq.