Open Access Research article

The RHNumtS compilation: Features and bioinformatics approaches to locate and quantify Human NumtS

Daniela Lascaro1, Stefano Castellana1, Giuseppe Gasparre2, Giovanni Romeo2, Cecilia Saccone1 and Marcella Attimonelli1*

Author Affiliations

1 Dipartimento di Biochimica e Biologia Molecolare "E. Quagliariello", Università di Bari, Via E. Orabona 4, 70126 Bari, Italy

2 Unità di Genetica Medica, Policlinico Universitario S. Orsola-Malpighi, Università di Bologna, 40138 Bologna, Italy

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BMC Genomics 2008, 9:267  doi:10.1186/1471-2164-9-267

Published: 3 June 2008

Additional files

Additional file 1:

Complete reference Human NumtS compilation (RHNumtS). A detailed legend is reported in Table 3.

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Additional file 2:

Comparison of BLAT and Megablast results. For each NumtS in the RHNumtS compilation, Megablast and BLAT programs either did or did not detect it (yes/no); if yes, table shows mt coordinates, BLAT code assigned, number of aligned blocks and fragments as reported in BLAT details, and %identity value as reported in BLAT output. NumtS reporting code "Yes_1" in "BLAT hits correspondence table" were recovered by submitting mt fragment corresponding to a NumtS obtained through Blastn to BLAT, and not through submission of entire mt genome (J01415.2 or NC_01807.4) to BLAT.

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Additional file 3:

Comparison between Reference Human NumtS compilation and some published compilations. Columns 2–7 list reference numbers, as reported in reference section. "-": absence of NumtS in corresponding reference, "OK": perfect match, "?" : partial match.

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Additional file 4:

Multi-alignments of sequenced NumtS from 4 different phylo-geographic samples. The nucleotide multi-alignments of the amplified (fig 2a in the manuscript) and sequenced NumtS 87, 122 and 41–54 of individuals coming from Europe, Japan, Latin America and North Africa belonging respectively to haplogroups H2b, G1a1a, I3a and L2a1c1 compared with the NumtS sequence as it can be extracted from the Human Genome build36.2 through the UCSC genome browser (hg18 release) and the sequences of the corresponding mitochondrial region for the same samples, are reported. Multi-alignments of NumtS 87 and 122 include the rCRS sequence (accession number J01415.2 in GenBank) also, thus allowing the exact localization of the variant sites respect to the universally used human mitochondrial reference sequence. As far as NumtS 41-54 the reference sequence has been added to NumtS 43 only in a distinctly reported multialignment. The conservation of NumtS is evident from the multialignment among the different subjects, although heterozygous sites can be observed (nucleotide ambiguity letter such as Y for C/T, R for A/G etc.). Each multi-alignment refers to the nuclear region (from Chromosome start to Chromosome end), as reported in additional file 1. The NumtS sequences produced in our validation experiments are named with a code defined by the NumtS code and the haplogroup of the sample. The corresponding mtDNA regions are coded as mt, followed by the haplogroup code. The reference sequence for 122 NumtS is extracted from Celera genome chromosome 9 (CM00260). Sequencing of L2a1c1 122 NumtS, H2b and L2a1c1 41, 42 and 54 NumtS failed.

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Additional file 5:

Sequences of 22 NumtS from a European sample (haplogroup L2a1c1). Each sequence has been multi-aligned with the NumtS sequence as it can be extracted from the Human Genome build36.2 through the UCSC genome browser (hg18 release), the sequence of the corresponding mitochondrial region for the same sample and the rCRS sequence (accession number J01415.2 in GenBank ). Each multi-alignment refers to the nuclear region (from Chromosome start to Chromosome end), as reported in additional file 1. The NumtS sequences produced in our validation experiments are named with a code defined by the NumtS code and the haplogroup of the sample. The corresponding mtDNA regions are coded as mt, followed by the haplogroup code.

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Additional file 6:

NumtS in RHNumtS featuring data. Scores obtained through application of NeedleN program. Chromosome map location, isochore family in which NumtS is located, name of gene and its region, if any, and NumtS location are all listed. NumtS are ordered according to decreasing length.

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Additional file 7:

Alignment results obtained with NeedlN and WaterN programs, available through EBI SRS server, compared with BLAT scores. Table shows results for each NumtS from both Needleman and Wunsch and Waterman and Smith algorithms for global and local alignments. Results of alignments are compared with BLAT scores. Each NumtS is identified by a numeric code in NumtS Code column. Columns list % similarity, % gaps, score, alignment length and ratio obtained by application of alignment programs. BLAT scores for each NumtS Code are shown in last column.

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