![]() The reverse complement of a DNA sequence refers to the reverse of the DNA sequence in which the original sequence’s base pairs have been inverted and the order of the bases has been reversed. ![]() This blog post posts a simple function to solve the problem – Enjoy it! 1 – What is a DNA sequence Reverse Complement? Below is a simple Python implementation of how the task can be accomplished. Pterobranchia Mitochondrial Code (pterobrachia_mitochondrial_genetic_code)Ģ5.Finding the reverse complement for DNA is a pretty common task in bioinformatics. Thraustochytrium Mitochondrial Code (thraustochytrium_mitochondrial_genetic_code)Ģ4. Scenedesmus obliquus Mitochondrial Code (scenedesmus_obliquus_mitochondrial_genetic_code)Ģ3. Trematode Mitochondrial Code (trematode_mitochondrial_genetic_code)Ģ2. Chlorophycean Mitochondrial Code (chlorophycean_mitochondrial_genetic_code)Ģ1. The Alternative Flatworm Mitochondrial Code (alternative_flatworm_mitochondrial_genetic_code)ġ6. ![]() The Ascidian Mitochondrial Code (ascidian_mitochondrial_genetic_code)ġ4. The Alternative Yeast Nuclear Code (alternative_yeast_nuclear_genetic_code)ġ3. The Bacterial, Archaeal and Plant Plastid Code (bacterial_plastid_genetic_code)ġ2. The Euplotid Nuclear Code (euplotid_nuclear_genetic_code)ġ1. The Echinoderm and Flatworm Mitochondrial Code (echinoderm_mitochondrial_genetic_code)ġ0. The Ciliate, Dasycladacean and Hexamita Nuclear Code (ciliate_nuclear_genetic_code)ĩ. The Invertebrate Mitochondrial Code (invertebrate_mitochondrial_genetic_code)Ħ. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code (mold_mitochondrial_genetic_code)ĥ. The Yeast Mitochondrial Code (yeast_mitochondrial_genetic_code)Ĥ. The Vertebrate Mitochondrial Code (vertebrate_mitochondrial_genetic_code)ģ. The Standard Code (standard_genetic_code)Ģ. The standard genetic code is ncbi_trans_table and others can be shown by show(ncbi_trans_table). The BioSequences package provides all NCBI defined genetic codes and they are registered in ncbi_trans_table. The translate function translates a sequence of codons in a RNA sequence to a amino acid sequence based on a genetic code. Translation is a slightly more complex transformation for RNA Sequences and so we describe it here in more detail. reverse instead of reverse!, and ungap instead of ungap!. Such methods are named the same, but without the exclamation mark. Many of these methods also have a version which makes a copy of the input sequence, so you get a modified copy, and don't alter the original sequence. This is useful in hashing/counting sequences in data that is not strand specific, and thus observing the short sequence is equivalent to observing its reverse complement. Base.push! - FunctionĪ canonical sequence is the numerical lesser of a k-mer and its reverse complement. In addition to setindex, many other modifying operations are possible for biological sequences such as push!, pop!, and insert!, which should be familiar to anyone used to editing arrays. This is called copy-on-write strategy and users don't need to care about it because it is transparent: If the user modifies a sequence with or subsequence, the job of managing and protecting the underlying data of sequences is handled for them. If and only if the data are shared, the subsequence creates a copy of itself. This is because modifying a sequence checks whether its underlying data are shared with other sequences under the hood. Julia> seq # but the original sequence is not Julia> subseq # the subsequence is modified Julia> subseq = DNA_T # modify the second element of it Julia> subseq = seq # create a subsequence from `seq` You may think that this is unsafe because modifying subsequences propagates to the original sequence, but this doesn't happen actually: julia> seq = dna"AAAA" # create a sequence Unlike Arrays in the standard library, creating this subsequence is copy-free: the subsequence simply points to the original LongSequence data with its range. Some types such as Kmer can be indexed using integers but not using ranges.įor LongSequence types, indexing a sequence by range creates a subsequence of the original sequence.
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