Pyrus Unigene v3

Overview
Analysis NamePyrus Unigene v3
Unigene NamePyrus Unigene v3
MethodCAP3
SourceGenbank Prunus pyrus ESTs (Jun 1, 2006)
Date performed2006-06-01

Many sequencing projects around the world are depositing ESTs from the genus Pyrus 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. The final assembly has been annotated by BLAST sequence similarity searching 2 against Swiss-Prot 3, TrEMBL 3, and TAIR 4's Arabidopsis proteins.

For more information on this project please contact the GDR development team.

All the Pyrus ESTs from GenBank on July 14, 2006 were included in this assembly. The parameters used for CAP3 were -p 90. CAP3 outputs assembled contigs and singlets. The number of tentative unigenes for this assembly is comprised of the combined contigs and singlets.

August 1st, 2006 : Genbank Rosaceae ESTs Assembled

 Processing Summary
 Number of ESTs available  335
 Number of ESTs available after filtering  330
 Average Length  423
 Number of Contigs(CAP3 Assembly, -p 90 )  35
 Average Length of Contigs  593
 Number of Singlets  236
 Number of Putative Unigenes  271

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 Pyrus ESTs used for this assembly were downloaded on June 14th, 2006

 

 EST Libraries
 Number of ESTs available  330
 # of Species  3
 # of Libraries  4
 # of Tissues  3
 # of Development Stages  2

 

View detailed chart of libraries.

 Species
 Pyrus communis  234
 Pyrus communis x Pyrus ussuriensis  81
 Pyrus pyrifolia  15

 

Homology

Homology was determined using the BLASTx algorithm for the Pyrus 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. 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 Pyrus Contigs
 Number of Contigs  35
 Number (%) of Contigs with a Match in Swiss-Prot Database
 Download Excel Spreadsheet
 13 (37.1%)
 Number (%) of Contigs with a Match in TrEMBL Database
 Download Excel Spreadsheet
 20 (57.1%)

 

 Homology of Pyrus Singlets
 Number of Singlets  236
 Number (%) of Singlets with a Match in Swiss-Prot Database
 Download Excel Spreadsheet
 115 (48.7%)
 Number (%) of Singlets with a Match in TrEMBL Database
 Download Excel Spreadsheet
 149 (63.1%)

 

Microsatellite Analysis

The type and frequency of simple sequence repeats in this unigene assembly (v3) 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.

Download data (SSRs, ORFs, and Primers) in Excel spreadsheet format:

 Sequence information
 Number of Sequences  330
 Number of Sequences Having One Or More SSRs  26
 Percentage of Sequences Having One Or More SSRs  7.9%
 Total Number of SSRs Found  26
 Number of Motifs  16

 

Frequency of Motif Type
 
 Motif Length  Frequency  Percentage Frequency
 2bp  16  61.5%
 3bp  6  23.1%
 4bp  2  7.7%
 5bp  2  7.7%

 

 

eSNP Summary

The type and frequency of single nucleotide polymorphisms in this unigene assembly (V3) were determined using the AutoSNP software package (Savage et al., 2005).

View autoSNP output:

 SNP Summary
 Number of Contigs  35
 Number of SNPs  1
 Consensus Size  20776 bp
 SNP Frequency  0.00/100 bp
 Total Transistions  1
 Total Transversions  0
 Total Indels  0

 

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.

Downloads
Sequence Files:
Blast Result Files:
Microsatellite Files: