Malus Unigene v4

Overview
Analysis NameMalus Unigene v4
Unigene NameMalus Unigene V4
MethodCAP3
SourceGenbank Malus ESTs (Jan 1, 2008)
Date performed2008-01-01

This is the fourth version of the Malus unigene. This build was used to develop oligos for generation of a Malus NimbleGen gene expression array which will be made publicly available to the community as soon as the array has been fully tested.  Many sequencing projects around the world are depositing ESTs from the genus Malus in the NCBI dbEST database.  The Malus ESTs included in this assembly were downloaded on January 1, 2008.

Not all of the Malus 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.

 

 Processing Summary
 Number of ESTs available  260,581
 Number of ESTs available after filtering  249,195
 Average Length  599
 Number of Contigs(CAP3 Assembly, -p 90 )  23,284
 Average Length of Contigs  860
 Number of Singlets  53,200
 Number of Putative Unigenes  76,484

 

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

 

 EST Libraries
 Number of ESTs available  260,930
 # of Species  5
 # of Libraries  115
 # of Tissues  55
 # of Development Stages  36

View detailed chart of libraries.

 Species
 Malus hybrid rootstock  321
 Malus sieboldii  1,210
 Malus pumila  8
 Malus x domestica  255,447
 Malus x domestica x Malus sieversii  3,944
 

 

Homology

Homology was determined using the BLASTx algorithm for the Malus 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 Malus Contigs
 Number of Contigs  23284
 Number (%) of Contigs with a Match in Swiss-Prot Database
 Download Excel Spreadsheet
 15284 (65.6%)
 Number (%) of Contigs with a Match in TrEMBL Database
 Download Excel Spreadsheet
 20505 (88.1%)

 

 Homology of Malus Singlets
 Number of Singlets  53200
 Number (%) of Singlets with a Match in Swiss-Prot Database
 Download Excel Spreadsheet
 22122 (41.6%)
 Number (%) of Singlets with a Match in TrEMBL Database
 Download Excel Spreadsheet
 35455 (66.6%)

 

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

 Sequence information
 Number of Sequences  249,195
 Number of Sequences Having One Or More SSRs  45,099
 Percentage of Sequences Having One Or More SSRs  18.1%
 Total Number of SSRs Found  56,356
 Number of Motifs  659

 

Frequency of Motif Type

 Motif Length  Frequency  Percentage Frequency
 2bp  26207  46.5%
 3bp  21002  37.3%
 4bp  7426  13.2%
 5bp  1721  3.1%
 

 

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  23284
 Number of SNPs  12949
 Consensus Size  20089759 bp
 SNP Frequency  0.06/100 bp
 Total Transistions  6859
 Total Transversions  3659
 Total Indels  2431
 

 

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.