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of blaKPC-2 and blaNDM-1 co-producing clinical isolates of Klebsiella pneumoniae in a Chinese teaching hospital JOURNAL Unpublished REFERENCE 2 (bases 1 to 11275) AUTHORS Wang,P., Hu,Y., Yi,G., Shen,X., Wang,Z., Ma,R., Shan,B. and Wang,Y. TITLE Direct Submission JOURNAL Submitted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