Extract genes from gbk file.

Question

[savscosta]

Hello everyone

I have several bacterial genomes files 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 "IVa2 protein".

Input:

 CDS             1879..3366
                 /gene="E1B"
                 /codon_start=1
                 /product="55K protein"
                 /protein_id="ADM66105.1"
                 /translation="MEPGHPTEQGLHPGLRSHAPVEGLDQAAGTENLELLASTASSSG
                 SSSSTQTNIHVGGRNEAGHGREPEERPGPSVGRGAGLNQVSSLYPELSKVLTSMARGV
                 KRERSDGGNTGMMTELTASLMNRKRPERLTWYELQQECRDELGLMQDKYGLEQIKTHW
                 LNPDEDWEEAIKKYAKIALRPDCKYIVTKTVNIRHACYISGNGAEVVIDTLDKAAFRC
                 CMMGMRAGVMNMNSMIFMNMKFNGEKFNGVLFMANSHMTLHGCSFFGFNNMCAEVWGA
                 SKIRGCKFYGCWMGVVGRPKSEMSVKQCVFEKCYLGVSTEGNARVRHCSSLETGCFCL
                 VKGTASLKHNMVKGCTDERMYNMLTCDSGVCHILKNIHVTSHPRKKWPVFENNLLIKC
                 HMHLGARRGTFQPYQCNFSQTKLLLENDAFSRVNLNGIFDMDVSVYKILRYDETKSRV
                 RACECGGRHTRMQPVALDVTEELRPDHLVMACTGTEFSSSGEDTD"
 gene            3454..3858
                 /gene="IX"
 CDS             3454..3858
                 /gene="IX"
                 /codon_start=1
                 /product="IX protein"
                 /protein_id="ADM66106.1"
                 /translation="MNGTGGAFEGGLFSPYLTTRLPGWAGVRQNVMGSTVDGRPVLPA
                 NSSTMTYATVGSSSLDSTAAAAAAAAAMTATRLASSYMPSSGSSPSVPSSIIAEEKLL
                 ALLAELEALSRQLAALTQQVSELREQQQQQNK"
 gene            complement(3902..5526)
                 /gene="IVa2"
 CDS             complement(join(3902..5235,5514..5526))
                 /gene="IVa2"
                 /codon_start=1
                 /product="IVa2 protein"
                 /protein_id="ADM66107.1"
                 /translation="METRGRRPCPFQHQQDESQAHPCKRPARGSPLHRDGDHPHSDPE
                 TLEGHDAGRAGRPSSRALQSQSSQPPKRGSLLDRDAVEHVTELWDRLELLSQTLAKMP
                 MADGLKPLKNFASLQELLSLGGDRLLGELVRENLQVRDMLNEVAPLLRDDGSCMSLNY
                 HLQPVIGVIYGPTGCGKSQLLRNLLSSQLITPAPETVFFIAPQVDMIPPSEMKAWEMQ
                 ICEGNFAPGPEGTIVPQSGTLRPKFIKMSYDDLTQEHNYDVSDPRNVFAKAAAHGPIA
                 IIMDECMENLGGHKGVSKFFHAFPSKLHDKFPKCTGYTVLVVLHNMNPRRDLGGNIAN
                 LKIQAKLHIISPRMHPSQLNRFANTYTKGLPVAISLLLKDIIQHHAQRPCYDWIIYNT
                 TPEHEAMQWCYLHPRDGLMPMYLNIQSHLYRVLEKIHRTLNDRERWTRAYRARKNK"
 gene            complement(5005..13458)
                 /gene="E2B"
 CDS             complement(join(5005..8526,13450..13458))
                 /gene="E2B"
                 /codon_start=1
                 /product="DNA polymerase"
                 /protein_id="ADM66108.1"
                 /translation="MALVQSHGARGLHAEAADPGCQPPRRRARQRSQGAAPGPARAPR
                 RRASAAPARGARTAAAAGSTPATPLLKAHRGTVVAPRSYGLMQCVDTTTNSPVEIKYH
                 LHLKHALTRLYEVNLRTLPPDLDLRDTMDSSQLRALVFALRPRRAEIWTWLPRGLVSL
                 SVLEEPQGESHAGEHESHQPGPPLLKFLLKGRAVYLVDEVQPVQRCEYCGRFYKHQHE
                 CSVRRRDFYFHHINSHSSNWWQEIQFFPIGSHPRTERLFVTYDVETYTWMGSFGKQLV
                 PFMLVMKFSGEPELVALARDLAVRLRWDRWERDPLTFYCVTPEKMAVGQQFRLFRDEL
                 QTLMARELWASFMQANPHLQEWALEQHGLQCPEDLTYEELKKLPHIKGRPRFMELYIV
                 GHNINGFDEIVLAAQVINNRASVPGPFRITRNFMPRAGKILFNDVTFALPNPLSKKRT
                 DFELWEHGGCDDSDFKYQFLKVMVRDTFALTHTSLRKAAQAYALPVEKGCCPYKAVNH
                 FYMLGSYRADDRGFPLREYWKDDEEYALNRELWEKKGEAGYDIIRETLDYCAMDVLVT
                 AELVAKLQDSYAHFIRDSVRLPHAHFNIFQRPTISSNSHAIFRQIVFRAEQPQRTNLG
                 PAFLAPSHELYDYVRASIRGGRCYPTYIGILSEPIYVYDICGMYASALTHPMPWGPPL
                 NPYERALAAREWQMALDDASSKIDYFDKELCPGIFTIDADPPDEHLLDVLPPFCSRKG
                 GRLCWTNEPLRGEVATSVDLVTLHNRGWRVRIVPDERTTVFPEWKCVAREYVQLNIAA
                 KERADRDKNQTMRSIAKLLSNALYGSFATKLDNKKIVFSDQMDESLLKSIAAGQANIK
                 SSSFLETDNLSAEVMPALEREYLPQQLALVDSDAEESEDEHRPAPFYTPPSGTPGHVA
                 YTYKPITFLDAEEGDMCLHTVEKVDPLVDNDRYPSHVASFVLAWTRAFVSEWSEFLYE
                 EDRGTPLQDRPIKSVYGDTDSLFVTERGHRLMETRGKKRIKKNGGKLVFDPEQPELTW
                 LVECETVCAHCGADAFAPESVFLAPKLYALQSLLCPACGRSSKGKLRAKGHAAEVLNY
                 ELMVNCYLADSQGEDRARFSTSRMSLKRTLASAQPGAHPFTVTETTLTRTLRPWKDMT
                 LAALDAHRLVPYSRSRPNPRNEEVCWIEMP"

output: gene complement(3902..5526) /gene="IVa2" CDS complement(join(3902..5235,5514..5526)) /gene="IVa2" /codon_start=1 /product="IVa2 protein" /protein_id="ADM66107.1" /translation="METRGRRPCPFQHQQDESQAHPCKRPARGSPLHRDGDHPHSDPE TLEGHDAGRAGRPSSRALQSQSSQPPKRGSLLDRDAVEHVTELWDRLELLSQTLAKMP MADGLKPLKNFASLQELLSLGGDRLLGELVRENLQVRDMLNEVAPLLRDDGSCMSLNY HLQPVIGVIYGPTGCGKSQLLRNLLSSQLITPAPETVFFIAPQVDMIPPSEMKAWEMQ ICEGNFAPGPEGTIVPQSGTLRPKFIKMSYDDLTQEHNYDVSDPRNVFAKAAAHGPIA IIMDECMENLGGHKGVSKFFHAFPSKLHDKFPKCTGYTVLVVLHNMNPRRDLGGNIAN LKIQAKLHIISPRMHPSQLNRFANTYTKGLPVAISLLLKDIIQHHAQRPCYDWIIYNT TPEHEAMQWCYLHPRDGLMPMYLNIQSHLYRVLEKIHRTLNDRERWTRAYRARKNK"

[Sishuo Wang]

hi,

you may want to try this one

[Joe]

Have you searched the forum? There are no end of solutions to parse out genes from Genbanks. Take a look at a the "Similar posts" on the right hand side of this page.

I would recommend you learn some BioPython or similar to achieve this.

[savscosta]

I already searched in various topics in the site. And I still have difficult to get this information from the gbk file.

Answer 1

[Joe]

As I mentioned, this question has been solved a lot on the forum:

A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC