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Overview
Analysis Name | Malus Unigene v4 |
Method | CAP3 |
Source | Genbank Malus ESTs (Jan 1, 2008) |
Date performed | 2008-01-01 |
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
- Huan, X. and Madan, A. (1999). CAP3: A DNA sequence assembly program. Genome Research, 9, 868-877.
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990) Basic local alignment search tool. J Mol Biol. 215(3):403-10.
- 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.
- 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.
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.
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% |
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Publication
No publications are currently available.
Downloads
Sequence Files: |
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Blast Result Files: |
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Microsatellite Files: |
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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).
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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 |
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