Question: Problem Fetching Genomic Sequence From Ddbj
1
gravatar for Woa
9.6 years ago by
Woa2.8k
United States
Woa2.8k wrote:

I'm trying to download some genomic sequences for a recently sequenced cell line(The article is open access) from DDBJ. The Accession nos. are AFTD00000000 and AFTD01000000 which can be found in this open access journal article under the 'Methods' section.

I tried the DDBJ Getentry but the FTP link it provides after an hour or of wait, points to an empty 36 bytes (!!??) file (Screenshot)

I also tried some of the Web-APIs of DDBJ from HERE, but without any results.

Can somebody suggest any other way to access the data?

Thanks in advance

WoA

sequence • 2.0k views
ADD COMMENTlink modified 9.6 years ago by Pierre Lindenbaum134k • written 9.6 years ago by Woa2.8k

I have no clue what is causing your problem since I never used DDBJ. But I always understood that all information in DDBJ is synchronized with Genbank and EMBL on a daily basis. now I am not sure whether that is true for whole genome sequences. But it is worth a try I guess. I actually would like to know whether sequences like this are synchronised.

ADD REPLYlink written 9.6 years ago by Chris Evelo10k

This is the corresponding NCBI entry, can someone tell how to get the genome sequence in a flat file? http://www.ncbi.nlm.nih.gov/nuccore/AFTD00000000

ADD REPLYlink written 9.6 years ago by Woa2.8k
2
gravatar for Pierre Lindenbaum
9.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum134k wrote:

as far as I understand, the sequences are available from:

http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AFTD01

there's a button "Show downloads", with a list of contigs available for download.

Genbank:

    wgs.AFTD.mstr.gbff.gz 1 kb
    wgs.AFTD.3.gbff.gz 217.2 Mb
    wgs.AFTD.2.gbff.gz 372.9 Mb
    wgs.AFTD.1.gbff.gz 381.4 Mb

FASTA:

    wgs.AFTD.1.fsa_nt.gz 263.9 Mb
    wgs.AFTD.2.fsa_nt.gz 258.1 Mb
    wgs.AFTD.3.fsa_nt.gz 148.9 Mb

test:

$ curl -s "ftp://ftp.ncbi.nlm.nih.gov//genbank/wgs/wgs.AFTD.3.fsa_nt.gz" | gunzip -c | head -n 20>gi|342520819|gb|AFTD01114121.1| Cricetulus griseus scaffold3292_20, whole genome shotgun sequence
CAGCCGCCGCGAACCAGCACGGACCACGGAGCCCTCCGGAGATGCCTCCCACACTTCCGAGAGCCGAAATGCGGAACCGA
CGAGATCTCGCGAGACTAGGCTTCCTCCGCCCCGCCCCGCGGTGCCTCGCTCCGCCCCTTACTGAGCTCAGCCAATCAGT
ATTCGGTGGGCCCGGGAAGGCCCTGGGGGGGGGGGCCAGTTCCGCCCTACGGTCAAGTATTCCGAGGCTGCGGGACGTCT
GCCAGCGCCGCTCGGTGACTGTTGTGCTATTTAGGGCTTCATTCTTTTTCTGAAGGAATACTATTGCAGCCACATCATCT
GTTGATGGACACTAGGGTGGTGTCTGCACGCGCATTACAATGCTGCTATGAGTGTTCATGTGCATGCTTTGCGCGCGTGA
AGAGAATGTGGGCACCAGGTGACACCACGGTAGAAATAAAGGAGGAGAAAGAAAATTGTGGAGATAAATAAATGGTGGGA
CAGGATGCGCAGTGGCAAAGACCCAGTACTTTCCCCGCTCTAACTGCTGGTGGTTTTAAACCATTCGAATGTCCCCTGTC
GCATTAATCGATTTTATTTTATCAACTGGTTTTCTTTTCTTTTTTCTTTCTTGTTGTTGCTCCTTTGTTGAGATAGGATA
TGACATAGCCCAAGATGCTTTAAAAGCTCAGTAAACAGCGGAGGATGACCTTGAATTCCTGATCCTCCTCCTCCCTCTGC
CTCCAAGTGCAGGGATTACAGGCTTGAGCTGCCATGCTGGGCTCCATCTATTAACTTTTAAAAACATTGTTTACAAATTT
GTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGTGTGTGTGTGTAAGAAAACATGTAGGAGT
TGGACCATGCCGGCGAGTGGGGTCCAACCAGGTTATCAGGCTTGTTCTGTAAGCTTTCTCATTTTATTTTTGTTTTATTA
ACATCTATAACGTCTGCAGTTTTATTTGTATGTGATTTAAAATGTATCTCTTGATAAAGGTTTATGGTTCTTCCTTTCTT
TTTCTGGTTCTTGAGACAGAGTTTCACTATGTAGTCCTACTGTCCTGGTACTCACTACATAGACCAGGATGTCCCCCAAA
CTCACAGAGATCTGCCGGCCTCTGCCTCTCTGCATTCTATTTATTCATTTTTTAATTATAATCTTTCCTCTTTTTTTCAA
TACAAGAGATTCTCTTTGTAGCCCTGACTATCTTGGAACTCAATCTGTAGACCAGACTAGCCTCAAACTCAGAGATCCAA
CTGCCTCTGCCTTCTGAGTGCAAGCTCCAGGACAACCAGGACTACATAGACCACCTCTCTCTCTCTCTCTCTCTCTCTCT
CTATATATATATATATATATATATGTGTGTGTGTGTGTGTGTGTGTATGTATGTATGTATATATGTGTGTGTATGTATGT
GTATATGTATATGTATTTATATATACATAATATATATATATATATATATATATGACTTGAGATACTGGAGAGATGGCTTA
ADD COMMENTlink written 9.6 years ago by Pierre Lindenbaum134k

Thanks Pierre!!

ADD REPLYlink written 9.6 years ago by Woa2.8k
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