Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • cliffbeall
    replied
    There is a tool on the IMG that generates Genbank format directly - there is a button at the bottom of the genome main page ("Taxon Details") saying Export Genome Data and Generate Genbank File. It worked ok for what I wanted, which was to look at the annotation with Artemis.

    The help says:

    #############################################

    This tool was provided to you as an aid. We do not guarantee the output is a valid Genbank format.
    You still need to spend extra effort to make the Genbank file accepted by NCBI. And we will no longer support this tool, why?

    You may generate a custom Genbank File for one or more scaffolds.
    Your MyIMG gene annotation may override the default product name.
    (You must be logged into MyIMG to use your annotations.)
    If an IMG term is associated with a gene, this can also override the product name.
    IMG term, if present and the override option selected, also overrides MyIMG annotation.

    Leave a comment:


  • EricSchon
    replied
    No module named BCBio

    Thanks!

    I tried to run the gff2genbank.py file from your github repository: https://github.com/chapmanb/bcbb/blo..._to_genbank.py

    However I get an import error:

    Traceback (most recent call last):
    File "gff2genbank.py", line 13, in <module>
    from BCBio import GFF
    ImportError: No module named BCBio

    I’ve tried to pip install

    (gff2genbank)[user@cluster scripts]$ pip install bcbio-gff
    Requirement already satisfied (use --upgrade to upgrade): bcbio-gff in /c3se/users/user/Glenn/virtualenvs/gff2genbank/lib/python2.7/site-packages
    Requirement already satisfied (use --upgrade to upgrade): six in /c3se/users/user/Glenn/virtualenvs/gff2genbank/lib/python2.7/site-packages (from bcbio-gff)
    Cleaning up...

    But it doesn’t help. Can you help me how to get the BCBio this module imported?

    Specs: non-sudo user on a CentOS release 6.6 distro. Python 2.7.6 and biopython 1.62

    Leave a comment:


  • GenoMax
    replied
    See if one of the following works


    Leave a comment:


  • EricSchon
    started a topic Getting genbank annotation file from JGI

    Getting genbank annotation file from JGI

    Hi All,

    I would like to extract the genbank or (embl) annotation file from genomes sequenced at JGI. At JGI you can download the annotation of the genomes in gff format, and you can get the genome or CDS in fasta format.

    So my question is:

    Is there any way of retrieving the genbank file from jgi or do I have to use a conversion tool to generate the genbank file myself from the gff and fasta files.

    If so, which conversion tool would you recommend (I guess people must have had this problem before, so I hope I don’t have to make a python converter myself)

    Thanks!

Latest Articles

Collapse

  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 02-23-2024, 04:11 PM
1 response
22 views
0 likes
Last Post kim897
by kim897
 
Started by seqadmin, 02-21-2024, 08:52 AM
0 responses
39 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-20-2024, 08:57 AM
0 responses
26 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-14-2024, 09:19 AM
0 responses
58 views
0 likes
Last Post seqadmin  
Working...
X