Fragaria Unigene v4

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

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

January 1st, 2008 : Genbank Rosaceae ESTs Assembled
 

 Processing Summary
 Number of ESTs available  50882
 Number of ESTs available after filtering  49132
 Average Length  651
 Number of Contigs(CAP3 Assembly, -p 90 )  5582
 Average Length of Contigs  969
 Number of Singlets  8314
 Number of Putative Unigenes  13896


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 Fragaria ESTs used for this assembly were downloaded on January 1st, 2008

 

 EST Libraries
 Number of ESTs available  50882
 # of Species  3
 # of Libraries  22
 # of Tissues  16
 # of Development Stages  8

 

View detailed chart of libraries.

 Species
 Fragaria vesca  42736
 Fragaria vesca subsp. vesca  2716
 Fragaria x ananassa  5430

 

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-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 Fragaria Contigs
 Number of Contigs  5582
 Number (%) of Contigs with a Match in Swiss-Prot Database
 Download Excel Spreadsheet
 4089 (73.3%)
 Number (%) of Contigs with a Match in TrEMBL Database
 Download Excel Spreadsheet
 5100 (91.4%)

 

 Homology of Fragaria Singlets
 Number of Singlets  8314
 Number (%) of Singlets with a Match in Swiss-Prot Database
 Download Excel Spreadsheet
 4092 (49.2%)
 Number (%) of Singlets with a Match in TrEMBL Database
 Download Excel Spreadsheet
 5986 (72.0%)

 

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.

 Sequence information
 Number of Sequences  49132
 Number of Sequences Having One Or More SSRs  9460
 Percentage of Sequences Having One Or More SSRs  19.3%
 Total Number of SSRs Found  12105
 Number of Motifs  333

 

Frequency of Motif Type
 
 Motif Length  Frequency  Percentage Frequency
 2bp  3345  27.6%
 3bp  6628  54.8%
 4bp  1513  12.5%
 5bp  619  5.1%

 

 

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  5582
 Number of SNPs  623
 Consensus Size  5420231 bp
 SNP Frequency  0.01/100 bp
 Total Transistions  252
 Total Transversions  137
 Total Indels  234

 

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.