Rosa Unigene V4
Many sequencing projects around the world are depositing ESTs from Rosa in the NCBI dbEST database. The Rosa ESTs included in this assembly were downloaded on January 1, 2008. 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.
The final assembly has been annotated by BLAST sequence similarity searching 2 against Swiss-Prot 3and TrEMBL 3. We will also provide homology information for TAIR 4's Arabidopsis proteins, Poplar and Vitis proteins in the near future.
For more information on this project please contact the GDR development team.
The Rosa ESTs used for this assembly were downloaded on January 1st, 2008
Homology was determined using the BLASTx algorithm for the Rosa Contigs and Singlets vs. the Swiss-Prot and TrEMBL databases. Only matches with an E-value of 1.0 e-6 or better were recorded. Swiss-Prot is a curated protein database with a high level of annotation and a minimal level of redundancy, and TrEMBL is a computer-annotated supplement of Swiss-Prot that contains all the translations of TrEMBL nucleotide sequence entries not yet integrated in Swiss-Prot.
Contig GO Terms
The GO Terms (www.geneontology.org) were determined by comparing the contigs against Swiss-Prot using BLAST. The Sprot2GO annotation file was then used to map go terms to the sequences using relevant matches (1e-9).
The type and frequency of simple sequence repeats in this unigene assembly (V4) were determined using the CUGIssr.pl program.For these searches, SSRs are defined as dinucleotides repeated at least 5 times, trinucleotides repeated at least 4 times, tetranucleotides repeated at least 3 times, or pentanucleotides repeated at least 3 times.
Frequency of Motif Type
The type and frequency of single nucleotide polymorphisms in this unigene assembly (V4) were determined using the AutoSNP software package (Savage et al., 2005).
View autoSNP output:
No publications are currently available.