Rubus Unigene v4

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

Many sequencing projects around the world are depositing ESTs from Rubus in the NCBI dbEST database. The Rubus 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  323
 Number of ESTs available after filtering  318
 Average Length  499
 Number of Contigs(CAP3 Assembly, -p 90 )  40
 Average Length of Contigs  576
 Number of Singlets  120
 Number of Putative Unigenes  160

 

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

 

 EST Libraries
 Number of ESTs available  348
 # of Species  2
 # of Libraries  3
 # of Tissues  2
 # of Development Stages  3

 

View detailed chart of libraries.

 Species
 Rubus idaeus  327
 Rubus idaeus subsp. strigosus  21

 

Homology

Homology was determined using the BLASTx algorithm for the Rubus 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 Rubus Contigs
 Number of Contigs  40
 Number (%) of Contigs with a Match in Swiss-Prot Database
 View as HTML | Download Excel Spreadsheet | Search
 25 (62.5%)
 Number (%) of Contigs with a Match in TrEMBL Database
 View as HTML | Download Excel Spreadsheet | Search
 30 (75.0%)

 

 Homology of Rubus Singlets
 Number of Singlets  120
 Number (%) of Singlets with a Match in Swiss-Prot Database
 View as HTML | Download Excel Spreadsheet | Search
 72 (60.0%)
 Number (%) of Singlets with a Match in TrEMBL Database
 View as HTML | Download Excel Spreadsheet | Search
 94 (78.3%)

 

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 Rubus sequence files (contigs, singlets or all ESTs) and run them against the GDR SSR server using your specific parameters.

 Sequence information
 Number of Sequences  318
 Number of Sequences Having One Or More SSRs  51
 Percentage of Sequences Having One Or More SSRs  16.0%
 Total Number of SSRs Found  64
 Number of Motifs  27

 

Frequency of Motif Type

 Motif Length  Frequency  Percentage Frequency
 2bp  27  42.2%
 3bp  23  35.9%
 4bp  14  21.9%
 5bp    

 

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  40
 Number of SNPs  7
 Consensus Size  23061 bp
 SNP Frequency  0.03/100 bp
 Total Transistions  6
 Total Transversions  1
 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.