Prunus Unigene v2

Analysis NamePrunus Unigene v2
SourceGenbank Prunus ESTs (Dec 1, 2005)
Date performed2005-12-01

Many sequencing projects around the world are depositing ESTs from the genus Prunus 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 Prunus 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  41900
 Number of ESTs available after filtering  40868
 Average Length  536.5
 Number of Contigs(CAP3 Assembly, -p 90 )  5047
 Average Length of Contigs  832.3
 Number of Singlets  7862
 Number of Putative Unigenes  12909



  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 Prunus ESTs used for this assembly were downloaded on December 19th, 2005


 EST Libraries
 Number of ESTs available  41900
 # of Species  5
 # of Libraries  27
 # of Tissues  11
 # of Development Stages  18


View detailed chart of libraries.

 Prunus armeniaca  15105
 Prunus avium  21
 Prunus cerasus  12
 Prunus dulcis  3864
 Prunus persica  22898



Homology was determined using the BLASTx algorithm for the Prunus 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 Prunus Contigs
 Number of Contigs  5041
 Number (%) of Contigs with a Match in Swiss-Prot Database
 Download Excel Spreadsheet
 3001 (59.5%)
 Number (%) of Contigs with a Match in TrEMBL Database
 Download Excel Spreadsheet
 4419 (87.6%)


 Homology of Prunus Singlets
 Number of Singlets  7862
 Number (%) of Singlets with a Match in Swiss-Prot Database
 Download Excel Spreadsheet
 2899 (36.9%)
 Number (%) of Singlets with a Match in TrEMBL Database
 Download Excel Spreadsheet
 2468 (31.4%)


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  40868
 Number of Sequences Having One Or More SSRs  8465
 Percentage of Sequences Having One Or More SSRs  20.7%
 Total Number of SSRs Found  11186
 Number of Motifs  385


Frequency of Motif Type
 Motif Length  Frequency  Percentage Frequency
 2bp  2937  26.3%
 3bp  6065  54.2%
 4bp  1741  15.6%
 5bp  443  4.0%



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.

Sequence Files:
Blast Result Files:
Microsatellite Files:


ESNP Summary

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:

 SNP Summary
 Number of Contigs  5047
 Number of SNPs  3776
 Consensus Size  4211138 bp
 SNP Frequency  0.09/100 bp
 Total Transistions  1838
 Total Transversions  1050
 Total Indels  888