ftp NCBI nucleotide database

[JQL]

Hi,

I tried to retrieve 400+ bacterial 16S rDNA sequences. I found them in the website.

How to find the same information in the ftp site? I can't seem to find the so-called nucleotide (or nuccore) database there.

I was hoping the download the 400+ files in batch and process them.

thanks,
John

[GenoMax]

Which 400 sequences are you referring to (perhaps linkout to SILVA SSU db)? The link you included is only for a single 16S sequence.

[JQL]

the genbank accession numbers: JN713151-JN713566

It is not silva database.

Which 400 sequences are you referring to (perhaps linkout to SILVA SSU db)? The link you included is only for a single 16S sequence.

[GenoMax]

Do you have access to nt blast database and blast+ programs? You can easily write a loop to extract the sequences using the following command (let me know if you need more details).

$ blastdbcmd -entry JN713152 -db /path_to/nt -outfmt '%f'

for i in {713151..713566}; do blastdbcmd -entry JN$i -db /path_to/nt -outfmt '%f' >> filename.fa; done

You can also use e-utilities (http://www.ncbi.nlm.nih.gov/books/NBK25500/) something along the lines of the example here: http://www.ncbi.nlm.nih.gov/books/NB...trieving_large

[JQL]

Hi GenoMax,

thank you very much for sharing that. I am going to ask our admin to install the database and BLAST+ and give it a try.

Will read the e-utilities too. I will get back to you.

Best,
John

[JQL]

Hi GenoMax,

Thanks for the tip. I got the db and it works -- got the fasta sequences! Now I have another question on how to retrieve the information under 'organism' tag. For example,
in this JN713151, I would also like to get the bacterial lineage (in red) for each query id. I tried many specifiers in the -help document, none has worked so far. Any thoughts?

John

LOCUS JN713151 1526 bp DNA linear ENV 09-MAY-2012
DEFINITION Filifactor alocis canine oral taxon 001 clone OB017 16S ribosomal
RNA gene, partial sequence.
ACCESSION JN713151
VERSION JN713151.1 GI:373279114
KEYWORDS ENV.
SOURCE Filifactor alocis
ORGANISM Filifactor alocis
Bacteria; Firmicutes; Clostridia; Clostridiales;
Peptostreptococcaceae; Filifactor.

[GenoMax]

You won't find that information in the blast database. Here is one way (I am sure there are others):

Save the following code in a file (e.g. retr.sh).

j=713151;
while [ $j -le 713567 ]
do
   num=`printf "JN%06d" $j`;
   curl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=${num}&rettype=genbank"
   j=$((j+1))
done

Add execute permissions to that file

$ chmod u+x retr.sh

Run the file to download genbank records.

$ ./retr.sh > genbank_records

Extract the ID information you need into a file (id_you_need).

$ grep -e JN -e OrgName_lineage genbank_records | sed 's/<Textseq-id_accession>//' | sed 's/<\/Textseq-id_accession>//' | sed 's/<OrgName_lineage>//' | sed 's/<\/OrgName_lineage>//' > id_you_need

[JQL]

Hi GenoMax,

thank you very much for your help and code. It works very nicely!

Just curious -- when the web download was extracted for locus id and lineage using grep, I found the locus id went beyond 713567, to all the way 713709 (in red below). Interestingly, those beyond 713566 were all human HIV virus lineage, not bacterial. I thought we only download
while [ $j -le 713567 ]? But anyway, it is easily cleaned up, not an issue, just wonder.

John

***
JN713566
Lachnospiraceae bacterium canine oral taxon 399 clone 1K033 16S ribosomal RNA gene, partial sequence</Seqdesc_title>
Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae
Human immunodeficiency virus 1 pol protein (pol) gene, partial cds.</Seqdesc_title>
Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus group
JN713567
HIV-1 isolate HIV_PRRT_PJ01967_1 from Dominican Republic pol protein (pol) gene, partial cds.</Seqdesc_title>
pol protein [Human immunodeficiency virus 1]</Seqdesc_title>
Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus group
JN713568
HIV-1 isolate HIV_PRRT_PJ01967_2 from Dominican Republic pol protein (pol) gene, partial cds.</Seqdesc_title>
pol protein [Human immunodeficiency virus 1]</Seqdesc_title>
Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus group
JN713569
HIV-1 isolate HIV_PRRT_PJ01967_3 from Dominican Republic pol protein (pol) gene, partial cds.</Seqdesc_title>
pol protein [Human immunodeficiency virus 1]</Seqdesc_title>
Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus group
JN713570