Fragaria Unigene v2

Many sequencing projects around the world are depositing ESTs from the genus Fragaria in the NCBI dbEST database. However, not all of these ESTs are of high quality. To filter, we crossmatched the public sequences against NCBI's UniVec database and used the BLAST sequence similarity algorithm to remove species-specific chloroplast, mitochondrial, tRNA, and rRNA sequences

To reduce redundancy and create longer transcripts we assembled these ESTs using the CAP3 ¹ program. For some sequences, we were able to obtain the original trace files and incorporate the phred quality values for each base into the assembly. We are in the process of annotating the final assembly through homology to Swiss-Prot, Arabidopsis, and NCBI nr proteins

For more information on this project please contact the GDR development team.

All the Fragaria ESTs from GenBank on December 19^th, 2005 were included in this assembly. The parameters used for CAP3 were -p 90. The CAP3 output generates assembled contigs and singlets. The number of tentative unigenes for this assembly is comprised of the combined contigs and singlets

December 19^th, 2005 : Genbank Rosaceae ESTs Assembled

References

1. Huan, X. and Madan, A. (1999). CAP3: A DNA sequence assembly program. Genome Research, 9, 868-877.
2. Boeckmann B., Bairoch A., Apweiler R., Blatter M.-C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., Pilbout S., and Sneider M. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Research. 31:365-370.
3. Pearson J.D. and Lipman,D.J. (1988). Improved tools for biological sequence comparison. Proc Natl Acad Sci USA, 85:2444-2448.