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Table 2 Differences in Blastn hit numbers by changing human genome searched datasets.

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

Limit by Entrez query

Hits#

Type of selected data reported in the Blastn output

6. – nothing

4903

Human Complete mt genomes, Human D-loop, other species

7. – Homo sapiens BUT NOT mitochondrion

2497

Genomic DNA, cDNA, D-loop also from other species

8. – Homo sapiens [ORGN]

4903

Human Complete mt genomes, D-loop,

9. – Homo sapiens [ORGN] NOT mitochondrion [PROP]

4903

Human Complete mt genomes, D-loop, other species

10. – Homo sapiens [ORGN] AND genomic DNA [MOLTYPE] NOT mitochondrion [PROP]

2154

Human Genomic DNA, cDNA, 2 complete mt genomes

11. – Homo sapiens [ORGN] NOT mitochondrion [ALL]

2497

Human Genomic DNA, cDNA, D-loop

12. – Homo sapiens [ORGN] AND genomic DNA [MOLTYPE] NOT mitochondrion [ALL]

123

Human Genomic DNA, cDNA

13. – Homo sapiens [ORGN] AND genomic DNA [MOLTYPE] NOT (mitochondrion OR mitochondrial) [ALL]

119

Human Genomic DNA

14. – nothing

16350

Genomic, D-loop, mt genomes other organisms

15. – Homo sapiens NOT mitochondrion

2097

Genomic DNA, D-loop, other organisms

16. – Homo sapiens [ORGN]

2106

Human Genomic DNA, D-loop, mt complete genomes

17. – Homo sapiens [ORGN] NOT (mitochondrion OR mitochondrial) [ALL]

2097

Human Genomic DNA, Human D-loop

18. – Homo sapiens [ORGN] NOT mitochondrion [PROP]

2154

2 human mt genomes, Genomic DNA

19. – Homo sapiens [ORGN] NOT (mitochondrion OR mitochondrial) [ALL]

2145

HGPC+Celera+Assemblychr7

20. – Homo sapiens [ORGN] NOT mitochondrion [ALL]

2145

HGPC+Celera

  1. Different Hits number and different class of selected entries obtained by changing subject sequence datasets through "Limits by Entrez query" function. Resulting subject sequences are subsets of non-redundant nucleotide database (query 6 to 13), ref_seq genome database (query 14 to 17), Chromosome human genome database (query 18 to 20) all available through Blastn at NCBI. E-value set at 0.001. Description#, graphic display# and alignments# were set at maximum values allowed. Runs 19 and 20, resulting in 2145 hits, were those most suited to our needs, i.e., to select completely assembled human nuclear sequences.