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Searching nucleotide databases for term with special character

Hi, I am trying to search some databases such as GenBank and EMBL-EBI for a search term that includes a colon. The problem is, even when I follow the advice to escape it with a backslash (https://www.ebi.ac.uk/ebisearch/documentation.ebi#query_syntax) it still doesn't include the colon in the string to search for, resulting in many results being included that I don't want. Does anyone know how to help?

database
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by lvogel • lvogel

which database/field are you searching ? If it's a DNA sequence, it would be easier to scan the files from a FTP server...

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written by Pierre Lindenbaum Pierre Lindenbaum

I'm searching for a term to be included in the organism name. It has the format [PREFIX]:[number] . There isn't a special field for it, but some entries do have it somewhere in the name. Those are the entries that I want. I am looking for DNA sequences, but I'm not searching the actual sequences right now. I'm trying to create a reference database. Interesting idea, though...

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written by lvogel • lvogel

1 answer

searching for a term to be included in the organism name. It has the format [PREFIX]:[number] 

wget -O taxdmp.zip ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip
unzip  taxdmp.zip names.dmp

$ grep -E  '\:[0-9]+' names.dmp | grep "scientific name" | tail
1897030 |   Firmicutes bacterium CAG:176_59_8   |       |   scientific name |
1897031 |   Firmicutes bacterium CAG:176_63_11  |       |   scientific name |
1897032 |   Firmicutes bacterium CAG:24053_14   |       |   scientific name |
1897033 |   Firmicutes bacterium CAG:272_52_7   |       |   scientific name |
1897034 |   Firmicutes bacterium CAG:321_26_22  |       |   scientific name |
1897035 |   Firmicutes bacterium CAG:552_39_19  |       |   scientific name |
1897036 |   Firmicutes bacterium CAG:65_45_313  |       |   scientific name |
1903134 |   Enterobacter sp. ST121:950178628    |       |   scientific name |
1905348 |   Platerodrilus sp. MNCN/DNA:86739    |       |   scientific name |
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written by Pierre Lindenbaum Pierre Lindenbaum

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