Question: Extract sequence from Genebank
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gravatar for anasofiamoreira94
11 weeks ago by
anasofiamoreira9450 wrote:

Hello, Can someone tell the way to extract the fasta sequences of gene 16S? Can I extract them in the genebank? Thanks

genebank • 148 views
ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by anasofiamoreira9450

A particular species or just 16S in general?

You can get the 16S microbial blast pre-formatted database here. You can extract the sequences from these file using blastdbcmd utility from BLAST+ package. Note: These sequences are from RefSeq targeted loci project.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by genomax75k

I have a number of particular species and I have to look for its fasta sequence according to the 16s. So my idea was to select only the gene 16s from mitochondrion in genebank.Do you think it is wrong? Thanks for the help.

ADD REPLYlink written 11 weeks ago by anasofiamoreira9450

Can you provide an example? There may be an Entrezdirect way to get this information.

ADD REPLYlink written 11 weeks ago by genomax75k

For instance, I want a fasta sequence of 16s for Acetes japonicus

ADD REPLYlink written 11 weeks ago by anasofiamoreira9450

Using EntrezDirect: For that organism there are only 14 sequences in Genbank and none of them are 16S. If you can use the following sequences then remove the last | grep part and replace with > file.fa.

$ esearch -db nuccore -query "Acetes japonicus [ORGN]" | efetch -format fasta | grep "^>"
>HQ630575.1 Acetes japonicus isolate AJ18_f_KK19 cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
>HQ630574.1 Acetes japonicus isolate AJ13_f_KK19 cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
>HQ630573.1 Acetes japonicus isolate AJ12_f_KG26 cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
>HQ630572.1 Acetes japonicus isolate AJ11_m_KG26 cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
>HQ630571.1 Acetes japonicus isolate AJ10_f_KG26 cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
>HQ630570.1 Acetes japonicus isolate AJ8_f_KG26 cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
>HQ630569.1 Acetes japonicus isolate AJ7_m_KG26 cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
>HQ630568.1 Acetes japonicus isolate AJ6_f_Tbhg18 cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
>HQ630567.1 Acetes japonicus isolate AJ5_m_Tbhg cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
>HQ630566.1 Acetes japonicus isolate AJ4_f_Tbhg cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
>HQ630565.1 Acetes japonicus isolate AJ3_m_tbhg cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
>HQ630564.1 Acetes japonicus isolate AJ2_f_Tbhg cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
>HQ630563.1 Acetes japonicus isolate AJ1_m_Tbhg cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
>KF977240.1 Acetes japonicus isolate DNZ050 cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by genomax75k

Ok,I will try that. But I'm having trouble using esearch, when I try to execute it, I get this error: WebEnv value not found in search output - WebEnv1 Db value not found in fetch input

ADD REPLYlink written 11 weeks ago by anasofiamoreira9450

Exact command above or something else?

ADD REPLYlink written 11 weeks ago by genomax75k

I used this command: esearch -db pubmed -query "lycopene cyclase" |efetch -format abstract

ADD REPLYlink written 11 weeks ago by anasofiamoreira9450

While this is unrelated to the original question, that command looks correct. I can get abstracts of papers by running the same command. There is going to be a lot of them so be careful.

ADD REPLYlink written 11 weeks ago by genomax75k
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