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This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2011

Open Access Research

Primates and mouse NumtS in the UCSC Genome Browser

Francesco Maria Calabrese, Domenico Simone and Marcella Attimonelli*

Author Affiliations

Dipartimento di Bioscienze, Biotecnologie e Scienze Farmacologiche, Università di Bari, Bari, 70126, Italy

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BMC Bioinformatics 2012, 13(Suppl 4):S15  doi:10.1186/1471-2105-13-S4-S15

Published: 28 March 2012

Additional files

Additional file 1:

RHNumtS.2 compilation. Human reference NumtS compilation on hg19 build. Each line refers to a NumtS and reports NumtS ID, HSP_NumtS ID, chromosome where NumtS is located, and strand where Blast mapped NumtS ("+" if in same direction as nuclear reference sequence, "-" if in opposite direction), chromosome and mitochondrial locations. For assembled NumtS (right), detailed information on each fragment is available. Last column shows identity percentage as reported in Blast output for each HSP.

Format: XLS Size: 162KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

RPNumtS compilation. Chimpanzee reference NumtS compilation on panTro2 build. Each line refers to a NumtS and gives NumtS ID, HSP_NumtS ID, chromosome where NumtS is located and strand where Blast mapped NumtS ("+" if in same direction as nuclear reference sequence, "-" if in opposite direction), chromosome and mitochondrial locations. For assembled NumtS (right), detailed information on each fragment is available. Last column shows identity percentage as reported in Blast output for each HSP.

Format: XLS Size: 194KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

RRNumtS compilation. Macaca mulatta reference NumtS compilation on rheMac2 build. Each line refers to a NumtS and gives NumtS ID, HSP_NumtS ID, chromosome where NumtS is located and strand where Blast mapped NumtS ("+" if in same direction as nuclear reference sequence, "-" if in opposite direction), chromosome and mitochondrial locations. For assembled NumtS (right), detailed information on each fragment is available. Last column shows identity percentage as reported in Blast output for each HSP.

Format: XLS Size: 175KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

RMNumtS compilation. Mus musculus reference NumtS compilation on mm9 build. Each line refers to a NumtS and gives NumtS ID, HSP_NumtS ID, chromosome where the NumtS is located and strand where Blast mapped NumtS ("+" if in same direction as nuclear reference sequence, "-" if in opposite direction), chromosome and mitochondrial locations. For assembled NumtS (right), detailed information on each fragment is available. Last column shows identity percentage as reported in Blast output for each HSP.

Format: XLS Size: 66KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

NumtS compilation comparisons. Differences in NumtS number and length (bp) in same species are due to different assembly and differences in parameters used to launch in silico hybridization. Discrepancies observed in both chimpanzee and rhesus macaque data between our results and those reported in [3], where the same assemblies and same e-value were used, cannot be explained, because information on Blast running in [3] is not complete. Instead, trend of differences observed in mouse match assembly time and parameters.

Format: PDF Size: 48KB Download file

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Open Data

Additional file 6:

RPNumtS annotation comparisons. Comparison were made by applying "Join" tool (UCSC Genome Browser) to compare our NumtS genomic intervals with those extracted from only previously published NumtS set available. Since this starting dataset contains orthologous NumtS only (human/chimpanzee orthologous), resulting output is partial. Data reported in [5] exactly match our data.

Format: XLSX Size: 78KB Download file

Open Data

Additional file 7:

NumtS and genome features correlation matrix. A Pearson correlation matrix was calculated to test significance of NumtS lengths in species examined, with respect to relative genome lengths.

Format: PDF Size: 34KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 8:

Figure 2 screenshots. This file provides magnified versions of screenshots shown in Figure 2.

Format: PDF Size: 1.7MB Download file

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