Fragaria Unigene v3

Overview
Analysis NameFragaria Unigene v3
MethodCAP3
SourceGenbank Fragaria ESTs (Jun 1, 2006)
Date performed2006-07-01

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. 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 Fragaria 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  19038
 Number of ESTs available after filtering  18729
 Average Length  636
 Number of Contigs(CAP3 Assembly, -p 90 )  2939
 Average Length of Contigs  871
 Number of Singlets  7073
 Number of Putative Unigenes  10012

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 June 14th, 2006

 

 EST Libraries
 Number of ESTs available  18729
 # of Species  2
 # of Libraries  12
 # of Tissues  6
 # of Development Stages  6

 

View detailed chart of libraries.

 Species
 Fragaria vesca  13453
 Fragaria x ananassa  5276

 

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. 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  2939
 Number (%) of Contigs with a Match in Swiss-Prot Database
 Download Excel Spreadsheet		  1827 (62.2%)
 Number (%) of Contigs with a Match in TrEMBL Database
 Download Excel Spreadsheet		  2435 (82.9%)

 

 Homology of Fragaria Singlets
 Number of Singlets  7073
 Number (%) of Singlets with a Match in Swiss-Prot Database
 Download Excel Spreadsheet		  2732 (38.6%)
 Number (%) of Singlets with a Match in TrEMBL Database
 Download Excel Spreadsheet		  4561 (64.5%)

 

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.

 Sequence information
 Number of Sequences  18729
 Number of Sequences Having One Or More SSRs  3821
 Percentage of Sequences Having One Or More SSRs  20.4%
 Total Number of SSRs Found  4947
 Number of Motifs  284

 

Frequency of Motif Type

 Motif Length  Frequency  Percentage Frequency
 2bp  1602  32.4%
 3bp  2536  51.3%
 4bp  588  11.9%
 5bp  211  4.5%

 

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.

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).

883 Contigs have Biological Process annotation:

1044 Contigs have Cellular Component annotation:

1252 Contigs have Molecular Function annotation:

 

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  2939
 Number of SNPs  342
 Consensus Size  2567433 bp
 SNP Frequency  0.01/100 bp
 Total Transistions  132
 Total Transversions  83
 Total Indels  127