Mercurial > repos > public-health-bioinformatics > match_plasmid_to_reference
diff test-data/CP008719.gbk @ 0:c917ef6807d7 draft default tip
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
author | public-health-bioinformatics |
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date | Tue, 12 Nov 2019 22:47:36 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CP008719.gbk Tue Nov 12 22:47:36 2019 -0500 @@ -0,0 +1,130 @@ +LOCUS CP008719 2101 bp DNA circular BCT 05-JAN-2016 +DEFINITION Escherichia coli strain ST648 plasmid pEC648_5, complete sequence. +ACCESSION CP008719 +VERSION CP008719.1 +DBLINK BioProject: PRJNA248607 + BioSample: SAMN02800875 +KEYWORDS . +SOURCE Escherichia coli + ORGANISM Escherichia coli + Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; + Enterobacteriaceae; Escherichia. +REFERENCE 1 (bases 1 to 2101) + AUTHORS Gao,Z. + TITLE Complete Genome Sequence of Multiple Antibiotic Resistant + Escherichia coli Isolated from Pleural Effusion of Patients with + Empyema Thoracis + JOURNAL Unpublished +REFERENCE 2 (bases 1 to 2101) + AUTHORS Gao,Z. + TITLE Direct Submission + JOURNAL Submitted (09-JUN-2014) Department of Respiratory and Critical care + medicine, Peking University People's hospital, Xizhimen South + Street, Beijing, Beijing 100101, China +COMMENT Annotation was added by the NCBI Prokaryotic Genome Annotation + Pipeline (released 2013). Information about the Pipeline can be + found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/ + + ##Genome-Assembly-Data-START## + Assembly Method :: Newbler v. 2.3; Consed + Genome Coverage :: 40x; 350x + Sequencing Technology :: Roche 454 GS FLX; Illumina Hiseq 2000 + ##Genome-Assembly-Data-END## + + ##Genome-Annotation-Data-START## + Annotation Provider :: NCBI + Annotation Date :: 06/13/2014 09:01:46 + Annotation Pipeline :: NCBI Prokaryotic Genome Annotation + Pipeline + Annotation Method :: Best-placed reference protein set; + GeneMarkS+ + Annotation Software revision :: 2.6 (rev. 437579) + Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; + repeat_region + Genes :: 4,807 + CDS :: 4,578 + Pseudo Genes :: 132 + CRISPR Arrays :: 2 + rRNAs :: 21 (5S, 16S, 23S) + tRNAs :: 72 + ncRNA :: 4 + Frameshifted Genes :: 116 + ##Genome-Annotation-Data-END## +FEATURES Location/Qualifiers + source 1..2101 + /organism="Escherichia coli" + /mol_type="genomic DNA" + /strain="ST648" + /db_xref="taxon:562" + /plasmid="pEC648_5" + gene join(1882..2101,1..47) + /locus_tag="FH07_00765" + CDS join(1882..2101,1..47) + /locus_tag="FH07_00765" + /inference="EXISTENCE: similar to AA + sequence:RefSeq:WP_001024536.1" + /note="Derived by automated computational analysis using + gene prediction method: Protein Homology." + /codon_start=1 + /transl_table=11 + /product="hypothetical protein" + /protein_id="ALV71377.1" + /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTF + GFHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS" + gene 913..1878 + /locus_tag="FH07_00775" + CDS 913..1878 + /locus_tag="FH07_00775" + /inference="EXISTENCE: similar to AA + sequence:RefSeq:WP_012421200.1" + /note="Derived by automated computational analysis using + gene prediction method: Protein Homology." + /codon_start=1 + /transl_table=11 + /product="Replication protein" + /protein_id="ALV71376.1" + /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRM + ASCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIV + VDYPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRG + KDGSAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGE + VVANVAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQL + DRETNEDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD" +ORIGIN + 1 tagatttaaa cggtatcaag tttggatttt taagaacgca ttcttagttc tggaaaagag + 61 ccagcggcag gctgaggtga taggtacgag attgcatgca atctctagtg ctctgtctat + 121 cctgcattat cctcagcatt atcctcagca ttatcctcag ccttgccaac tcgacaccaa + 181 tgcaggatag acaatccgat gtcaaatgtt aacactctgc gagtggtaca ttttccccgg + 241 attatcgtcc tgagcctgcc gctggctctc tttctaccgc ctcgctttgc tcgttgctca + 301 acgcctcaca gacacggatt aaaatccgca tccgttcacc gttttttaaa gtccgttaaa + 361 agcatgatgc catctccgag agttaatctc gtcaaatgct aaatcgtggg ggtccccttt + 421 ggggttccga tttagtgatt gacgacacca ccgattaaaa aacttatgcg gggtggatgg + 481 tttcacgaag tgaggccatc cacctgtaag acagggtttt gtttttattc cctgttttgg + 541 tgatcgggtg tgtggaaaag gttggggtaa gccgttcggg ggtgcttgtt ttggggggtt + 601 aaaattgtgg ttattttttg cgcaattctc gcgcgtgatc cttgtattta tacttaaggg + 661 ataaatggcg gatatgaaat agtggtttag cccagtaatg acgaggcttt gagtgggttt + 721 tgacaggtca aagaaaatgg agcagaattg aggcgttttt aatcggcgtt ggggagtgcg + 781 tcaacactcc ccaacatttc gaatgtgtca cctcagcggc aaactctggt gacatgtact + 841 ggctcgcaat gcacaggtac gtgatgaata taccacatca aatcacagcc tgcccagatc + 901 ggagcaggct taatgtcaga agataaattc ctttcggact acagcccccg tgatgcagtt + 961 tgggataccc agcgcacgct taccgattct gtcgggggta tctaccagac tgctgctgaa + 1021 ttcgagcgct atgcactccg tatggcctcc tgtagcggtt tgttacgttt tggttggtct + 1081 accatcatgg aaaccggaga aacgcgccta cggcttcgta gtgcgcaatt ttgccgtgtc + 1141 cgtcattgcc ctgtctgcca gtggagaaga accctcatgt ggcaagcccg tttttatcag + 1201 gctctaccga aaatcgttgt ggattacccg tcttcccgat ggttgtttct gacgttaact + 1261 gtcaggaact gcgagatagg tgaacttgga acagtcctta cagcaatgaa tgcggcgttt + 1321 aagcgaatgg aaaagcgaaa ggagctatca cctgttcagg ggtggatcag ggctacggag + 1381 gtgacgcgag gtaaggatgg cagcgcacat ccgcattttc actgtctgct gatggtgcaa + 1441 ccttcttggt ttaaagggaa gaactacgtt aagcacgaac gttgggtaga actctggcgc + 1501 gattgcttgc gggtgaacta tgagccgaat atcgatattc gggcagtaaa aactaagaca + 1561 ggtgaggttg tggccaacgt tgccgagcaa ctgcaaagcg cggttgctga aacgctgaaa + 1621 tactccgtta aaccggaaga tatggcaaac gatcctgagt ggtttcttga gctgacgcgg + 1681 cagcttcaca agcgccgttt tatctcgacc ggtggggcgc taaaaaacgt cctccagttg + 1741 gatcgagaaa ccaatgagga tcttgtcatt gccgacgatg taggggatgg cactgatgac + 1801 gggaagcgga cggcgtttgt ctgggattca ggtaaacggc gttacaaacg cgcccctgag + 1861 aaggataaat cggattaacg tatgaatatt aatattgaat acctgaatgg aaataagact + 1921 attggtttat tttttttaag aagtgaagcg gtgattcctg acaggtttaa aaaccttatt + 1981 ttgcttattg atggattaag ttttggcaca tttggttttc atccgcacga aggttttgag + 2041 gatgaattaa ttttatatat tcagaaaaca aacgagaggg taaaaactct ttttgtgaaa + 2101 a +// +