Table 2

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

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


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.

Lascaro et al. BMC Genomics 2008 9:267   doi:10.1186/1471-2164-9-267

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