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Old 10-21-2019, 12:29 PM   #1
savisco
Junior Member
 
Location: Brazil

Join Date: Oct 2019
Posts: 1
Unhappy Genes from GBK

I have a list of genes and i want to obtain all the information in CDS and GENE from a genome in .gbk format.
I am trying to find some script or software that will allow me to get the part of the gbk file referring to the names of several genes.

For example of this file. And i want to obtain just the part of the product with name "korC".
Code:
Input:
LOCUS       MH558576               11275 bp    DNA     linear   BCT 03-SEP-2018
DEFINITION  Klebsiella pneumoniae strain KP21-KPC plasmid, partial sequence.
ACCESSION   MH558576
VERSION     MH558576.1
KEYWORDS    .
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella.
REFERENCE   1  (bases 1 to 11275)
  AUTHORS   Wang,P., Hu,Y., Yi,G., Shen,X., Wang,Z., Ma,R., Shan,B. and Wang,Y.
  TITLE     Clone dissemination of blaKPC-2 and blaNDM-1 co-producing clinical
            isolates of Klebsiella pneumoniae in a Chinese teaching hospital
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 11275)
  AUTHORS   Wang,P., Hu,Y., Yi,G., Shen,X., Wang,Z., Ma,R., Shan,B. and Wang,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-JUL-2018) Department of Key Laboratory, The 2nd
            Affiliated Hospital of Kunming Medical University, 374 Dian Mian
            Road, Kunming, Yunnan 650101, China
COMMENT     ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..11275
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="KP21-KPC"
                     /isolation_source="urine"
                     /db_xref="taxon:573"
                     /plasmid="unnamed"
                     /country="China: Kunming,YN"
                     /collection_date="2010"
     CDS             43..759
                     /codon_start=1
                     /transl_table=11
                     /product="IS6-like element IS26 family transposase"
                     /protein_id="AXS01185.1"
                     /translation="MELHSRVFEM"
     gene            862..1272
                     /gene="tnpR"
                     /note="truncated TnpR resolvase"
     CDS             1395..2375
                     /codon_start=1
                     /transl_table=11
                     /product="IS481-like element ISKpn27 family transposase"
                     /protein_id="AXS01186.1"
               /translation="MTQALHSQARTTHLIREEIRNSTLPQAELARMYNVTRQTIRKWQ
                     EKRPELFRKRVYNQPGLDI"
     gene            2651..3532
                     /gene="kpc"
                     /note="carbapenem-hydrolyzing class A beta-lactamase
                     KPC-2"
     CDS             2651..3532
                     /gene="kpc"
                     /codon_start=1
                     /transl_table=11
                     /product="carbapenem-hydrolyzing class A beta-lactamase
                     KPC-2"
                     /protein_id="AXS01187.1"
                     /translation="MSLYRRLVLLSCLSYVNGQ"
     gene            complement(4767..5063)
                     /gene="korC"
                     /note="transcriptional repressor protein KorC"
     CDS             complement(4767..5063)
                     /gene="korC"
                     /codon_start=1
                     /transl_table=11
                     /product="transcriptional repressor protein KorC"
                     /protein_id="AXS01188.1"
                     /translation="MIRPETLRSKTNPSPIAYGAWSILAHLAGFGAIWDADRD"
     gene            complement(5392..5817)
                     /gene="klca"
                     /note="antirestriction protein"
     CDS             complement(5392..5817)
                     /gene="klca"
                     /codon_start=1
                     /transl_table=11
                     /product="antirestriction protein"
                     /protein_id="AXS01189.1"
                     /translation="MMQTELNPLICSLVRDWACEHDEKEAILAAID"
     CDS             complement(5928..6206)
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="AXS01190.1"
                     /translation="MIHTANRTFHQLYRSLELNKMWLSWREKK"
     CDS             7749..8309
                     /codon_start=1
                     /transl_table=11
                     /product="TnpR resolvase"
                     /protein_id="AXS01191.1"
                     /translation="MQGHRIGALAKQRGAYRGRKKALSDEQAATLRQRATA
                     GEPKAQLAREFNISRETLYQYLRTDD"
     CDS             8313..>11275
                     /codon_start=1
                     /transl_table=11
                     /product="Tn3-like element TnAs1 family transposase"
                     /protein_id="AXS01192.1"
                     /translation="MPRREHINLTGDYVWRQSR
                     RLEDGKFRPLRMPGKP"

output:
Code:
   gene            complement(4767..5063)
                     /gene="korC"
                     /note="transcriptional repressor protein KorC"
     CDS             complement(4767..5063)
                     /gene="korC"
                     /codon_start=1
                     /transl_table=11
                     /product="transcriptional repressor protein KorC"
                     /protein_id="AXS01188.1"
                     /translation="MIRPETLRSKTNPSPIAYGAWSILAHLAGFGAIWDADRD"

Last edited by GenoMax; 10-30-2019 at 11:16 AM. Reason: Added [code] tags
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Old 10-30-2019, 09:38 AM   #2
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

What do you want to do with the text snippet next?

Can you program? If so, I would suggest looking at Biopython, BioPerl or a similar library which has a GenBank parser. They would let you parse the GenBank file, and select the feature with name korC, and do something with it - be that just print it out, or further processing.
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