Prunus Unigene v4

Overview
Analysis NamePrunus Unigene v4
Unigene NamePrunus Unigene v4
MethodCAP3
SourceGenbank Prunus ESTs (Jan 1, 2008)
Date performed2008-01-01

Many sequencing projects around the world are depositing ESTs from Prunus in the NCBI dbEST database. The Prunus 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.

 

 Processing Summary
 Number of ESTs available  92421
 Number of ESTs available after filtering  89166
 Average Length  568
 Number of Contigs(CAP3 Assembly, -p 90 )  9179
 Average Length of Contigs  919
 Number of Singlets  15128
 Number of Putative Unigenes  24307

 

References

  1. Huan, X. and Madan, A. (1999). CAP3: A DNA sequence assembly program. Genome Research, 9, 868-877.
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990) Basic local alignment search tool. J Mol Biol. 215(3):403-10.
  3. 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.
  4. Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P. (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gate way to Arabidopsis biology, research materials and community. Nucleic Acids Res.. 31(1):224-8.

 

 

 

 
Library Information
The Prunus ESTs used for this assembly were downloaded on January 1st, 2008

 EST Libraries
 Number of ESTs available  89,166
 # of Species  7
 # of Libraries  39
 # of Tissues  21
 # of Development Stages  20

View detailed chart of libraries.

 Species
 Prunus armeniaca  15105
 Prunus avium  21
 Prunus avium x cerasus x canescens  89
 Prunus cerasus  1255
 Prunus dulcis  3864
 Prunus domestica  54
 Prunus persica  70939
 

 

Homology

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-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.

 Homology of Prunus Contigs
 Number of Contigs  9179
 Number (%) of Contigs with a Match in Swiss-Prot Database
 Download Excel Spreadsheet
 5,944 (64.8%)
 Number (%) of Contigs with a Match in TrEMBL Database
 Download Excel Spreadsheet
 8,241 (89.8%)

 

 Homology of Prunus Singlets
 Number of Singlets  15,128
 Number (%) of Singlets with a Match in Swiss-Prot Database
 Download Excel Spreadsheet
 5,782 (38.2%)
 Number (%) of Singlets with a Match in TrEMBL Database
 Download Excel Spreadsheet
 9,511 (62.9%)
 

 

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).

 

 

 

 

Microsatellite Analysis

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. If you would like to different microsatellite motif parameters download the Prunus sequence files (contigs, singlets or all ESTs) and run them against the GDR SSR server using your specific parameters.

 Sequence information
 Number of Sequences  89166
 Number of Sequences Having One Or More SSRs  21005
 Percentage of Sequences Having One Or More SSRs  23.6%
 Total Number of SSRs Found  28178
 Number of Motifs  585

 

Frequency of Motif Type

 Motif Length  Frequency  Percentage Frequency
 2bp  9020  32.0%
 3bp  13914  49.4%
 4bp  3784  13.4%
 5bp  1460  5.2%
 

 

eSNP Summary

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:

 

 SNP Summary
 Number of Contigs  9,179
 Number of SNPs  5,852
 Consensus Size  8,454,286 bp
 SNP Frequency  0.07/100 bp
 Total Transistions  2,637
 Total Transversions  1,525
 Total Indels  1,690
 

 

Contact
 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
 Email  dorrie@wsu.edu
 

 

Publication

No publications are currently available.