Comparison of Genomic DNA to cDNA Alignment Methods
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This document compares different genomic DNA alignment methods, including a classic semi-global algorithm and heuristic tools like sim4 and Spidey. It analyzes the performance of these aligners on subsets of human gene and mRNA data, evaluating metrics like number of gaps, exon differences, sequence similarity, and runtime. The results show that the classic semi-global aligner produces very high-quality alignments but is slow, while sim4 achieves good accuracy faster than other external tools and outperforms them on most metrics.
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Comparison of Genomic DNA to cDNA Alignment Methods
- 1. Comparison of Genomic DNA to cDNA Alignment Methods Miguel Galves and Zanoni Dias Institute of Computing Unicamp Campinas SP Brazil {miguel.galves,zanoni}@ic.unicamp.br Scylla Bioinformatics Campinas SP Brazil {miguel,zanoni}@scylla.com.br
- 2. Agenda Introduction Problem Aligners Data set Subsets Evaluation Methods Results: Exact Alignments Results: EST Alignments Running Time Comparison Conclusions
- 3. Introduction Identifying genes in non-characterized DNA sequences is one of the greatest challenges in genomics EST-to-DNA alignment is one of the most common methods EST are key to understanding the inner working of an organism Human being has between 30000 and 35000 genes Alternative Splicing plays an important role in diversity
- 4. CCCGGGAAACGAAUAU CCUCUCACCCGGGA CUUGGCCCGGGAAACGAAUAU CCUCUCACCCGGG A CUUGG Problem Mature mRNA mRNA Intron Exon
- 5. Problem: How to solve ? Classic algorithms Dynamic programming Heuristic based algorithms Multi-steps Based on other tools such as Blast and local alignments.
- 6. Aligners Java version of global and semi-global Affine gap penalty function Linear space Global algorithm by Miller and Myers (1988) Semi-global based on global algorithm Heuristic based algorithms sim4, Spidey and est_genome
- 7. Data Set Human genome database Based on FASTA a GENBANKs flat format file from NCBI repository. Filtering criteria Genes, mRNAs and CDS with /pseudo tag mRNAs without any CDS Genes without any mRNA CDS matching wrong patterns 23124 genes and 27448 mRNAs stored in database
- 8. Subsets Subset 1Subset 1:: 66 genes from chromossome Y whith less than 100000 bases Subset 2: 50 complete genes from chromossome Y whith less than 100000 bases Subset 3: 8056 complete genes from all chromossomes whith less than 100000 bases Subset 4: 493 artificial EST based on complete genes from chromossome 6 with less than 100000 bases
- 9. Evaluation methods Number of gaps introduced in the aligned gene sequence Delta exons Bases similarity percentage Mismatch percentage
- 10. Experimental method Two score systems, from 15 previously defined and an alignment strategy were choosed, using subsets 1 and 2: Semi-global aligner (1,-2,-1,0) and (1,-2,-10,0) score systems The classic semi-global aligner was compared to sim4, Spidey and est_genome, both with subsets 3 and 4
- 11. Results: Exact Alignments Extra Gap Strategy Avg SD %Score 0 SG(1, -2, -1, 0) 0.00 0.00 100.00% SG(1, -2, -10, 0) 0.00 0.00 100.00% sim4 1.11 1.63 54.56% est_genome 16.99 21.49 27.84% Spidey 0.15 1.39 97.43%
- 12. Results: Exact Alignments Delta Exons Strategy Avg SD %Score 0 SG(1, -2, -1, 0) 0.00 0.00 100.00% SG(1, -2, -10, 0) 0.01 0.07 99.91% sim4 -0.01 0.20 97.46% est_genome -0.14 0.30 76.79% Spidey -4.04 3.10 0.00%
- 13. Results: Exact Alignments Base Similarity Strategy Avg SD %Scr. 100% SG(1, -2, -1, 0) 99.89% 0.49% 53.56% SG(1, -2, -10, 0) 99.89% 0.49% 53.49% sim4 99.39% 1.34% 22.79% est_genome 53.83% 35.00% 18.11% Spidey 80.34% 36.49% 44.25%
- 14. Results: Exact Alignments Mismatch Percentage Strategy Avg SD %Scr. 100% SG(1, -2, -1, 0) 0.00% 0.00% 100.00% SG(1, -2, -10, 0) 0.01% 0.03% 99.47% sim4 0.17% 0.21% 36.68% est_genome 1.19% 1.26% 21.55% Spidey 0.15% 0.98% 90.65%
- 17. Running Time Comparison EST-to-DNA (sec/alignment) mRNA-toDNA (sec/alignment) sim4 0.013 0.170 Spidey 0.066 0.140 est_genome 0.640 3.400 Semi-global 0.670 5.170
- 18. Conclusions Classic semi-globl algorithm produces good results Running time is a problem, although it can be improved Sim4 produces the best results amont external softwares tested
- 19. Thanks