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restgenomeanalysisenglish [2014/08/12 00:22]
haruo
restgenomeanalysisenglish [2014/12/13 08:25] (current)
haruo
Line 124: Line 124:
   * http://​rest.g-language.org/​NC_000913/​rRNA/​16S (shows a list of feature IDs of 16S rRNAs)   * http://​rest.g-language.org/​NC_000913/​rRNA/​16S (shows a list of feature IDs of 16S rRNAs)
   * http://​rest.g-language.org/​NC_000913/​get_geneseq/​FEATURE462 (shows nucleotide sequence of 16S rRNA with FEATURE462)   * http://​rest.g-language.org/​NC_000913/​get_geneseq/​FEATURE462 (shows nucleotide sequence of 16S rRNA with FEATURE462)
 +
 +
 +====== Pattern searches ======
 +The [[http://​www.g-language.org/​documentation/​1.9.0/​lib/​G/​Seq/​PatSearch.html|PatSearch]] class is a collection of sequence analysis methods related to pattern searches for oligonucleotides,​ including [[http://​rest.g-language.org/​help/​oligomer_search|oligomer_search]] and [[http://​rest.g-language.org/​help/​palindrome|palindrome]]. For example, you can search an [[https://​en.wikipedia.org/​wiki/​Inverted_repeat#​Palindrome_vs._inverted_repeat|inverted repeat]] (5' TTACGnnnnnnCGTAA 3') and palindrome (5' TTACGCGTAA 3') as follows.
 +
 +For //E.coli// (ecoli),
 +http://​rest.g-language.org/​ecoli/​oligomer_search/​TTACGCGTAA
 +searches for an oligomer "​TTACGCGTAA"​ and returns list of positions where oligomers are found as follows.
 +  209570,​1164188,​1443204,​1934579,​2167198,​2919269,​4203297
 +
 +http://​rest.g-language.org/​ecoli/​oligomer_search/​TTACGnnnnnnCGTAA/​return=both
 +searches for an inverted repeat "​TTACGnnnnnnCGTAA"​ and returns both positions and oligomers as follows.
 +  843936,​ttacgaaacagcgtaa,​3112312,​ttacgcacaggcgtaa
 +
 +Oligomer can be specified using degenerate code (e.g. "​grtggngg"​) or regular expressions (e.g. "​g[ag]tgg[a-z]gg"​).
 +
 +http://​rest.g-language.org/​plasmidf/​palindrome/​shortest=10
 +searches 10-bp or longer palindrome sequences in plasmid F (plasmidf)
  
  
restgenomeanalysisenglish.txt ยท Last modified: 2014/12/13 08:25 by haruo