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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".
output:
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:
[I]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JOURNAL Unpublished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"[/I]
output:
Code:
[I]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"[/I]
Comment