Fragaria Unigene v2

Overview
Analysis NameFragaria Unigene v2
Unigene NameFragaria Unigene v2
MethodCAP3
SourceGenbank Fragaria ESTs (Dec 1, 2005)
Date performed2005-12-01

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

 Processing Summary
 Number of ESTs available  9399
 Number of ESTs available after filtering  9213
 Average Length  536.6
 Number of Contigs(CAP3 Assembly, -p 90 )  1372
 Average Length of Contigs  687.7
 Number of Singlets  4193
 Number of Putative Unigenes  5565

 

References

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

 

 EST Libraries
 Number of ESTs available  9399
 # of Species  2
 # of Libraries  11
 # of Tissues  7
 # of Development Stages  6

 

View detailed chart of libraries.

 Species
 Fragaria vesca  4023
 Fragaria x ananassa  5376

 

Homology

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.

 Homology of Fragaria Contigs
 Number of Contigs  1372
 Number (%) of Contigs with a Match in Swiss-Prot Database
 Download Excel Spreadsheet
 676 (49.3%)
 Number (%) of Contigs with a Match in TrEMBL Database
 Download Excel Spreadsheet
 901 (65.7%)

 

 Homology of Fragaria Singlets
 Number of Singlets  4193
 Number (%) of Singlets with a Match in Swiss-Prot Database
 Download Excel Spreadsheet
 1298 (31.0%)
 Number (%) of Singlets with a Match in TrEMBL Database
 Download Excel Spreadsheet
 1241 (29.6%)

 

Microsatellite Analysis

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.

 Sequence information
 Number of Sequences  9213
 Number of Sequences Having One Or More SSRs  1462
 Percentage of Sequences Having One Or More SSRs  15.9%
 Total Number of SSRs Found  1835
 Number of Motifs  193

 

Frequency of Motif Type

 Motif Length  Frequency  Percentage Frequency
 2bp  647  35.3%
 3bp  836  45.6%
 4bp  279  15.2%
 5bp  73  4.0%

 

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  1372
 Number of SNPs  283
 Consensus Size  949734 bp
 SNP Frequency  0.03/100 bp
 Total Transistions  115
 Total Transversions  69
 Total Indels  99

 

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: