Rosaceae Family Unigene v2

Analysis NameRosaceae Family Unigene v2
SourceGenbank Rosaceae ESTs (Dec 1, 2005)
Date performed2005-12-01

Many sequencing projects around the world are depositing ESTs from the genus Rosaceae 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 Rosaceae 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

Processing Summary
 Number of ESTs available  259827
 Number of ESTs available after filtering  251253
 Average Length  594
 Number of Contigs(CAP3 Assembly, -p 90 )  10478
 Average Length of Contigs  1032.6
 Number of Singlets  61636
 Number of Putative Unigenes  72114


  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


Library Information
The Rosaceae ESTs used for this assembly were downloaded on December 19th, 2005


 EST Libraries
 Number of ESTs available  259827
 # of Species  16
 # of Libraries  134
 # of Tissues  55
 # of Development Stages  56


View detailed chart of libraries.

 Malus ESTs  202888
 Prunus ESTs  41900
 Fragaria ESTs  9399
 Rosa ESTs  5305
 Pyrus ESTs  227



Homology was determined using the BLASTx algorithm for the Rosaceae 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.

 Homology of Rosaceae Contigs
 Number of Contigs  23340
 Number (%) of Contigs with a Match in Swiss-Prot Database
 Download Excel Spreadsheet
 10376 (44.5%)
 Number (%) of Contigs with a Match in TrEMBL Database
 Download Excel Spreadsheet


 Homology of Rosaceae Singlets
 Number of Singlets  35103
 Number (%) of Singlets with a Match in Swiss-Prot Database
 Download Excel Spreadsheet
 8869 (25.3%)
 Number (%) of Singlets with a Match in TrEMBL Database
 Download Excel Spreadsheet


Microsatellite Analysis

The type and frequency of simple sequence repeats in this unigene assembly (v2) were determined using the 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.

 Sequence information
 Number of Sequences  72114
 Number of Sequences Having One Or More SSRs  14292
 Percentage of Sequences Having One Or More SSRs  19.8%
 Total Number of SSRs Found  16382
 Number of Motifs  643


Frequency of Motif Type
 Motif Length  Frequency  Percentage Frequency
 2bp  8330  43.8%
 3bp  6896  36.3%
 4bp  2958  15.6%
 5bp  835  4.4%



 Contact Details
 Name  Main, Dorrie
 Lab  Department of Horticulture
 Organization  Washington State University
 Address  45 Johnson Hall, Pullman, WA 99164
 Telephone  509-335-2774
 Fax  509-335-8690



No publications are currently available.

ESNP Summary

eSNP Summary not availble for Rosaceae Assembly V2