{"id":1507,"date":"2023-03-08T00:41:27","date_gmt":"2023-03-07T15:41:27","guid":{"rendered":"https:\/\/bdsl.jbnu.ac.kr\/blog\/?p=1507"},"modified":"2023-03-08T00:57:56","modified_gmt":"2023-03-07T15:57:56","slug":"genbank-flat-file","status":"publish","type":"post","link":"https:\/\/bdsl.jbnu.ac.kr\/blog\/genbank-flat-file\/","title":{"rendered":"GenBank Flat File"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Example of GenBank Flat File format<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>NCBI GenBank Flat File Format Sample record: https:\/\/www.ncbi.nlm.nih.gov\/Sitemap\/samplerecord.html<\/li>\n\n\n\n<li>Example file: <a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/03\/sequence.txt\">genbank_example<\/a><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Handling GenBank Flat File<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">Load a .gb file <\/h3>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">import os\r\nfrom skbio import DNA, RNA, sequence\r\n\r\ndna_seq = DNA.read('.\/sequence.gb')<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">Display information on the sequence<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"adoc\" class=\"language-adoc\">DNA\r\n----------------------------------------------------------------------\r\nMetadata:\r\n    'ACCESSION': 'AH002671 K02214 M18715 M18717 M18719 M18721 M18723\r\n                  M18725 M18727 M18782 M18784 M18786'\r\n    'COMMENT': &lt;class 'str'>\r\n    'DEFINITION': 'Homo sapiens alpha-amylase (AMY1) gene, complete\r\n                   cds; and AMY1A gene, complete sequence.'\r\n    'KEYWORDS': 'alpha-amylase; amylase.'\r\n    'LOCUS': &lt;class 'dict'>\r\n    'REFERENCE': &lt;class 'list'>\r\n    'SOURCE': &lt;class 'dict'>\r\n    'VERSION': 'AH002671.2'\r\nInterval metadata:\r\n    41 interval features\r\nStats:\r\n    length: 3429\r\n    has gaps: False\r\n    has degenerates: True\r\n    has definites: True\r\n    GC-content: 29.05%\r\n----------------------------------------------------------------------\r\n0    GCATTCAAGT TAACTCTTCC CCTTGGTATC TGTACATACC TTTGATGTCA GTGTTTAGTA\r\n60   CACGTGGCTT GGTCACTTCA TGGCTAAAAA CGTGCTTGTG GAAGACAAGT CTGGCTTGGT\r\n...\r\n3360 TGCTGAATCT AAATTGTAAA ATTTAAAATT AAATGCAAAT CCGCAAAGCA ATAGCTAAGT\r\n3420 GTGTTTCTT\r\n<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">Display accession numbers<\/h3>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">dna_seq.metadata['ACCESSION']<\/code><\/pre>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">'AH002671 K02214 M18715 M18717 M18719 M18721 M18723 M18725 M18727 M18782 M18784 M18786'\r<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">Display sequences<\/h3>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">str(dna_seq)<\/code><\/pre>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">'GCATTCAAGTTAACTCTTCCCCTTGGTATCTGTACATACCTTTGATGTCAGTGTTTAGTACACGTGGCTTGGTCACTTCATGGCTAAAAACGTGCTTGTGGAAGACAAGTCTGGCTTGGTGAGTCTGTGTGGTCAGCAGTCTCTGATCCGTGCAGGGTATTAATGTGTCAGGGCTGAGTGTTCTGAGATTTATCTAGAGGCTGGGAAGGGCTCCTGAACCAGTTGTTTCCGTCTTGTCGGTCTGTCAGGGTTGGAAAGTCCAAGCCATAGGACCCAGTTTCCTTTCTTAGCTTACGTTATCTACCAGAGCACCGTGGGCTGTTACTTGCCTTGAGTTGGAAGCGGTTCGCATTTATACCGGTAAATGTATTCATCCTTTTAATTTATGTAAAGTTTTTTAGTATGCAATTCTCGATCTTTTAAGAGTTGACAACAAATTTTGGTTTTCTGCTGTTATGTGAGAACATTAGGCCACAGCAACATGTCATTGTGTAAGGAAAAATAAAAGTGCTACCATATGCAAAAAAAAAAAAAAAAAGAAAAGAAAAGAAACATTAATGTCTAAGAGGTCATTGAGATGATTTCCATGAGAGACTTTTTGATGTTCTTCACCAGTTAGGATTATTATTGATAATCCTTTTCAGATTATGAATAAACAGTTTGCCCTCAAGTATTTATTCATGCTACTATTTACATTGTAAAATGTGCTTCTTACAGGAATATAAATAGTTTCTGGAAAGGACACTGACAACTTCAAAGCAAAATGAAGCTCTTTTGGTTGCTTTTCACCATTGGGTTCTGCTGGGCTCAGTATTCCTCAAATACACAACAAGGACGAACATCTATTGTTCATCTGTTTGAATGGCGATGGGTTGATATTGCTCTTGAATGTGAGCGATATTTAGCTCCCAAGGGATTTGGAGGGGTTCAGGTGGGTATGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAATTTGTAGGTCTCTCCACCAAATGAAAATGTTGCCATTCACAACCCTTTCAGACCTTGGTGGGAAAGATACCAACCAGTTAGCTATAAATTATGCACAAGATCTGGAAATGAAGATGAATTTAGAAACATGGTGACTAGATGCAACAATGTTGGGGTAAGTGAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGTTTTCTAGGTTCGTATTTATGTGGATGCTGTAATTAATCATATGTGTGGTAATGCTGTGAGTGCAGGAACAAGCAGTACCTGTGGAAGTTACTTCAACCCTGGAAGTAGGGACTTTCCAGCAGTCCCATATTCTGGATGGGATTTTAATGATGGTAAATGTAAAACTGGAAGTGGAGATATCGAGAACTATAATGATGCTACTCAGGTAATTTTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACCTCAACAGGTCAGAGATTGTCGTCTGTCTGGTCTTCTCGATCTTGCACTGGGGAAGGATTATGTGCGTTCTAAGATTGCCGAATATATGAACCATCTCATTGACATTGGTGTTGCAGGGTTCAGAATTGATGCTTCCAAGCACATGTGGCCTGGAGACATAAAGGCAATTTTGGACAAACTGCATAATCTAAACAGTAACTGGTTCCCGGAAGGTAGTAAACCTTTCATTTACCAGGAGGTACGTCAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTCTTCTAGGTAATTGATCTGGGTGGTGAGCCAATTAAAAGCAGTGACTACTTTGGTAATGGCCGGGTGACAGAATTCAAGTATGGTGCAAAACTCGGCACAGTTATTCGCAAGTGGAATGGAGAGAAGATGTCTTACTTAAAGTAAATAAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCAAAAATAGGAACTGGGGAGAAGGTTGGGGTTTCATGCCTTCTGACAGAGCGCTTGTCTTTGTGGATAACCATGACAATCAACGAGGACATGGCGCTGGAGGAGCCTCTATACTTACCTTCTGGGATGCTAGGTAAAAAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAACTTTCAGGCTGTACAAAATGGCAGTTGGATTTATGCTTGCTCATCCTTATGGATTTACACGAGTAATGTCAAGCTACCGTTGGCCAAGATATTTTGAAAATGGAAANGTAAGTTTTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGTAATTAAGGATGTTAATGATTGGGTTGGGCCACCAAATGATAATGGAGTAACTAAAGAAGTTACTATTAATCCAGACACTACTTGTGGCAATGACTGGGTCTGTGAACATCGATGGCGCCAAATAAGGTGAGAATATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTGTTTTTAGGAACATGGTTAATTTCCGCAATGTAGTGGATGGCCAGCCTTTTACAAACTGGTATGATAATGGGAGCAACCAAGTGGCTTTTGGGAGAGGAAACAGAGGATTCATTGTTTTCAACAATGATGACTGGTAAGTAAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTATTTTACAGGACATTTTCTTTAACTTTGCAAACTGGTCTTCCTGCTGGCACATACTGTGATGTCATTTCTGGAGATAAAATTAATGGCAACTGCACAGGCATTAAAATCTACGTTTCTGATGATGGCAAAGCTCATTTTTCTATTAGTAACTCTGCTGAAGATCCATTTATTGCAATTCATGCTGAATCTAAATTGTAAAATTTAAAATTAAATGCAAATCCGCAAAGCAATAGCTAAGTGTGTTTCTT'<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>Example of GenBank Flat File format Handling GenBank Flat File Load a .gb file Display information on the sequence Display accession numbers Display 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