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Open Access Highly Accessed Research article

SIS: a program to generate draft genome sequence scaffolds for prokaryotes

Zanoni Dias1, Ulisses Dias1 and João C Setubal23*

Author Affiliations

1 Instituto de Computação, Universidade Estadual de Campinas, Campinas, SP, Brazil

2 Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil

3 Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA

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BMC Bioinformatics 2012, 13:96  doi:10.1186/1471-2105-13-96

Published: 14 May 2012

Additional files

Additional file 1:

Figure S1. Variation in the Number of Correct Adjacencies (Top 1). Variation in the number of correct adjacencies determined by each scaffold program when the reference genome is the closest to the query genome. The diamond is the median. Figure S2. Variation in the Number of Correct Adjacencies (Top 10). Variation in the number of correct adjacencies determined by each scaffold program averaged over the 10 closest genomes to the query genome. The diamond is the median. Figure S3. Variation in the Number of Correct Adjacencies (Top 20). Variation in the number of correct adjacencies determined by each scaffold program averaged over the 20 closest genomes to the query genome. The diamond is the median. Figure S4. Test Cases X Correct Adjacencies (Top 1). Figure S5. Test Cases X Correct Adjacencies (Top 10). Figure S6. Test Cases X Correct Adjacencies (Top 20). Figure S7. Correct Adjacencies X Number of Contigs (Top 1). Figure S8. Correct Adjacencies X Number of Contigs (Top 10). Figure S9. Correct Adjacencies X Number of Contigs (Top 20). Figure S10. Example of Dotplot. Pairwise whole genome comparison of two Pseudomonas species. The comparison was done using nucmer [18]. Figure S11.Mycobacterium (All pairs). Variation of the distribution of the number of correct adjacencies in the scaffolds generated by the various programs for the complete set (210 pairs) of Mycobacterium genomes. Figure S12.Pseudomonas (All Pairs). Variation of the distribution of the number of correct adjacencies in the scaffolds generated by the various programs for the complete set (153 pairs) of Pseudomonadaceae genomes. Figure S13.Shewanellas (All Pairs). Variation of the distribution of the number of correct adjacencies in the scaffolds generated by the various programs for the complete set (190 pairs) of Shewanella genomes. Figure S14.Xanthomonas (All Pairs). Variation of the distribution of the number of correct adjacencies in the scaffolds generated by the various programs for the complete set (36 pairs) of Xanthomonas genomes. Figure S15.Mycobacterium (Best Pairs). Variation of the distribution of the number of correct adjacencies in the scaffolds generated by the various programs for only those pairs of Mycobacterium genomes that are closest to each other in the second batch of tests. Figure S16.Pseudomonas (Best Pairs). Variation of the distribution of the number of correct adjacencies in the scaffolds generated by the various programs for only those pairs of Pseudomonas genomes that are closest to each other in the second batch of tests. Figure S17.Shewanellas (Best Pairs). Variation of the distribution of the number of correct adjacencies in the scaffolds generated by the various programs for only those pairs of Shewanella genomes that are closest to each other in the second batch of tests. Figure S18.Xanthomonas (Best Pairs). Variation of the distribution of the number of correct adjacencies in the scaffolds generated by the various programs for only those pairs of Xanthomonas genomes that are closest to each other in the second batch of tests. Figure S19. Average (All Pairs). Variation of the distribution of the average number of correct adjacencies in the scaffolds generated by the various programs for the complete set of test instances in the second batch. Figure S20. Average (Best Pairs). Variation of the distribution of the average number of correct adjacencies in the scaffolds generated by the various programs for only those pairs of genomes that are closest to each other in the second batch of tests.

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