Question: GI chromosome list ncbi
0
gravatar for TEman
4.0 years ago by
TEman10
Sweden
TEman10 wrote:

Hi,

I am using Entrez.efetch in BioPython to fetch sequences from genomic coordinates (chr, start, stop, strand):

  handle = Entrez.efetch(db="nucleotide",
                       id=[GI number],
                       rettype="fasta",
                       strand=strand,
                       seq_start=start,
                       seq_stop=stop)
    record = SeqIO.read(handle,"fasta")

    handle.close()

    print record.seq
   

The package requires the GI of the chromosomes, but I don't know how to find these. Tried to manually search in the nucleotide database in ncbi, but this gives a lot of different GIs for each chromosome.

I am looking for the most recent mus musculus genomic sequences.

Any suggestions how to get these GIs or another way to circumvent this problem?

Best

Per

sequence genome • 1.5k views
ADD COMMENTlink modified 4.0 years ago by genomax70k • written 4.0 years ago by TEman10
1
gravatar for genomax
4.0 years ago by
genomax70k
United States
genomax70k wrote:

One way to do this is to grab the RefSeq ID's for the chromosomes from the genome page: http://www.ncbi.nlm.nih.gov/genome/52

NC_000067.6
NC_000068.7
NC_000069.6
NC_000070.6
NC_000071.6
NC_000072.6
NC_000073.6
NC_000074.6
NC_000075.6
NC_000076.6
NC_000077.6
NC_000078.6
NC_000079.6
NC_000080.6
NC_000081.6
NC_000082.6
NC_000083.6
NC_000084.6
NC_000085.6
NC_000086.7
NC_000087.7
NC_005089.1

Then use the blastdbcmd utility along with the blast indexes for refseq_genomic blast indexes

$ blastdbcmd -entry_batch file_with_refseq_ID -db /path_to/refseq_genomic -outfmt "%g"

to get the GI #

372099109
372099108
372099107
372099106
372099105
372099104
372099103
372099102
372099101
372099100
372099099
372099098
372099097
372099096
372099095
372099094
372099093
372099092
372099091
372099090
372099089
34538597
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by genomax70k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 539 users visited in the last hour