Genbank accession number + nucleotide position to genomic coordinates
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5 months ago
Basti ▴ 80

Hi everyone,

I have a list of Genbank accession number with nucleotides positions extracted from several articles that I would like to convert into genomic coordinates and I don't know if this is possible. For exemple I have these accession number + nucleotide position :

AF125183: 7877–8096
AL117190: 51004–51262
Y10620: 609–827

Do you have any tips on how yould proceed to obtain genomic coordinates from this ? Thanks in advance to those who can enlighten me!

genbank genome number accession • 238 views
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5 months ago
GenoMax 108k

You can try EntreDirect (assuming these are all gene accessions). You will need to map the actual intervals if you are looking for a strict 1:1 co-ordinate mapping.

$ esearch -db nuccore -query "Y10620" | elink -target gene | efetch -format tabular
tax_id  Org_name    GeneID  CurrentID   Status  Symbol  Aliases description other_designations  map_location    chromosome  genomic_nucleotide_accession.version    start_position_on_the_genomic_accession end_position_on_the_genomic_accession   orientation exon_count  OMIM
9606    Homo sapiens    4232    0   live    MEST    PEG1    mesoderm specific transcript    mesoderm-specific transcript homolog protein|paternally-expressed gene 1 protein    7q32.2  7       NC_000007.14    130486175   130506465   plus    15  601029

Just the coordinates

$ esearch -db nuccore -query "Y10620" | elink -target gene | efetch -format tabular | awk -F "\t" '{OFS="\t"}{print $11,$12,$13,$14}'
chromosome  genomic_nucleotide_accession.version    start_position_on_the_genomic_accession end_position_on_the_genomic_accession
7   NC_000007.14    130486175   130506465
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That is perfect thank you so much !

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