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 19th, 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 19th, 2005 : Genbank Rosaceae ESTs Assembled
The Fragaria ESTs used for this assembly were downloaded on December 19th, 2005
Homology was determined using the BLASTx algorithm for the Fragaria Contigs and Singlets vs. the Swiss-Prot and TrEMBL databases. Only matches with an E-value of 1.0 e-9 or better were recorded as significant. 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 EMBL nucleotide sequence entries not yet integrated in Swiss-Prot.
The type and frequency of simple sequence repeats in this unigene assembly (v2) 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 (V2) were determined using the AutoSNP software package (Savage et al., 2005).
View autoSNP output:
No publications are currently available.