Question: Rast Genes All In The Forward Direction
0
gravatar for Lee Katz
8.2 years ago by
Lee Katz3.0k
Atlanta, GA
Lee Katz3.0k wrote:

Hi, I uploaded my own gene predictions via a genbank file to RAST (preview of the genbank file below). RAST changed every single gene except for some RNA genes to the forward direction.

When I used RAST without my gene predictions and uploaded only the assembly in fasta format, genes were correctly oriented.

Question: how would I alter my genbank file so that RAST respects the directionality of each gene?

LOCUS       scaffold3/1           168998 bp    dna     linear   BCT
DEFINITION   XXXXX, unfinished sequence, whole genome shotgun sequence
ACCESSION   unknown
KEYWORDS    WGS.
SOURCE      Vibrio cholerae
  ORGANISM  Vibrio cholerae
            Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales;
            Vibrionaceae; Vibrio.
FEATURES             Location/Qualifiers
     gene            complement(942..259)
                     /locus_tag="2011EL-1144H_draft_0312"
     CDS             complement(942..259)
                     /locus_tag="2011EL-1144H_draft_0312"
                     /evidence=predicted
                     /translation="[removed for brevity here in biostar]"
                     /transl_table=11
                     /note="Predictors: gmhmmp, Glimmer3, BLAST"
annotation • 1.5k views
ADD COMMENTlink modified 6.7 years ago by Biostar ♦♦ 20 • written 8.2 years ago by Lee Katz3.0k
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