Reverse Complement converts a DNA sequence into its reverse, complement, or reverse-complement counterpart. If one needs to convert back to string to interface with the rest of the code, what is the impact on speed ? Get regions' information from DNA sequence data (bsgenome.hsapiens.ucsc.hg19), What is the best way to get a large number of RNA seq data from SRA in Python without being denied access. It's good that this one actually included the code for that, though. from Bio import SeqIO records = (rec.reverse_complement(id="rc_"+rec.id, description = "reverse complement") \ for rec in SeqIO.parse("example.fasta", "fasta") if len(rec)<700) SeqIO.write(records, "rev_comp.fasta", "fasta") … Teams. For the sequence, this uses the Seq object’s reverse complement method. By the way, I get output like this. seq CATGTAGACTAG is 12 bases long reverse complement is CTAGTCTACATG protein translation is HVD* This was a very quick demonstration of Biopython’s Seq (sequence) object and some of its methods. I'm not sure how a Python 2 Cython setup compares. For this exercise, try using a dictionary structure to loop over the data. ... Biopython v: 1.75 Versions Previous Latest If you feel like contributing to this in the future, check out the github page I made for this question. ; id - The primary ID used to identify the sequence – a string. This tries to balance easy of use with worries about what to do with the annotation in the reverse complemented record. There are plenty of questions that need to be answered, just make sure that you are really addressing what the person have asked :-), Sorry. Print the GC content of each sequence. if directionsToConsider in ("reverse","both"): # consider reverse complement DNA sequence as well # start translation from 1, 2 and 3 nucleotide for frame in range(3): trans = str(seq.reverse_complement()[frame:].translate(tranlationTable)) allPossibilities.append(trans) # Count the number of stop codons in each frame When I asked the question, I had not considered whether I would allow for cython or c extensions when selecting the final answer. Stack Overflow for Teams is a private, secure spot for you and your coworkers to find and share information. and it appears it does, making it among the best performers so far! This means you need your DNAStrings to be in bytes instead of a string and so it would need a separate generation function. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. A nucleotide sequence can be reverse complemented to get a new sequence. How can I adjust the vertical positioning of \lim so the argument is aligned with the whole limit stack rather than just the word "lim"? Each thread would work on "rc"-ing sequences in its own piece of the array. Write a Biopython script that reads in a FASTA file, and prints a new FASTA file with the reverse complement of each sequence. The Seq object has a number of methods which act just like those of a Python string, for example the find method: You do not need the more advanced string encoding capabilities of string to store a string of bases, but you're still paying for it in performance. Making statements based on opinion; back them up with references or personal experience. I suggested working with bytes instead of strings throughout. ... You will however need to handle yourself the reverse complement, and maybe introns, if you need to worry about them. Hint. Note some of these methods described here are only available in Biopython 1.49 onwards. I have a DNA sequence and would like to get reverse complement of it using Python. The four lines below were taken from Biopython cookbook, and the script works perfectly well. By default the new record does NOT preserve the sequence identifier, name, description, general annotation or database cross-references - these are unlikely to apply to the reversed sequence. Asking for help, clarification, or responding to other answers. Similarly, the complemented sequence can be reverse complemented to get the original sequence. Below is a basic example for calculating GC content: Transcription: It is basically a process of converting a DNA into a RNA sequence. Biopython’s SeqIO (Sequence Input/Output) interface can be used to write sequences to files. seq - The sequence itself, typically a Seq object. The SeqIO.write() function can write an entire list of SeqIO records. Some of the advanced operations are listed below . Introduction¶. If one were already reading sequences in using biopython, though, I wouldn't be surprised if the performance was much different. The Seq object also provides some biological methods, such as complement, reverse_complement, transcribe, back_transcribe and translate (which are not applicable to sequences with a protein alphabet). Note that Biopython 1.44 and earlier would give a truncated version of repr(my_seq) for str(my_seq). If you need to go string->bytes->string then it is about 25-30% slower than staying with strings. However, in Biopython and bioinformatics in general, we typically work directly with the coding strand because this means we … @bli It is still about 10% faster if you can work with bytes all the way through and then transfer to a string at the end. The most reliable and simplest way is probably using Biopython: As Devon has already said here using Biopython isn't as fast as the naive Python solution, and I also tested that shown here with ipython. Why did the US have a law that prohibited misusing the Swiss coat of arms? How do I politely recall a personal gift sent to an employee in error? I don't doubt that your code works, but I am a bit sceptical if it answers the original question (seeking for fastest solution). For those wondering, using biopython is slower for this (~50% slower than the naive implementation), presumably due to the overhead of converting the strings to Seq objects. Reverse-complementing SeqRecord objects¶ One of the new features in Biopython 1.57 was the SeqRecord object’s reverse_complement method. The reverse_complement() method complements and reverses the resultant sequence from left to right. Q&A for Work. Edit: Great answers, everyone! What is the fastest way to get the reverse complement of a DNA sequence in python? @Devon_Ryan: With this test bench, the "Cython implementation (v2)" on my Python 3 setup gave a 91.1% increase over baseline and "table" (translate) gave a 84.6% increase. @Chris_Rands True, updated with the change needed for python3 (thankfully, it's only a single line difference). reverse_complement (Retrieving annotations from GenBank file. I didn't think to do that. code. @JackAidley I mentioned in my own reply that biopython is ~50% slower than the naive code in the original post. On my mac I get 800k strings converted with that implementation ("biopython just rc") when using the benchmark . In Biopython it is very easy to get both of a sequence. From the biopython website their goal is to “make it as easy as possible to use Python for bioinformatics by creating high-quality, reusable modules and scripts.” These modules use the biopython tutorial as a template for what you will learn here. Many handle sequence data and common analysis and processing of the data including reading and writing all common file formats. Nucleotide sequence can be reverse complemented to get new sequence. Dear all, I have a problem with Biopython. Here's a Cython approach that might suggest a generic approach to speeding up Python work. It is shown below − Biopyt… In Biopython, the base DNA strand is directly converted to mRNA simply by changing the letter T with U. And it appears it does, making it among the best performers so far that code! Module of Biopython provides the ambiguous_dna_complement variable which is used to identify the sequence – a string and then maketrans... Is used to perform the complement operations T with U is about 25-30 slower. Already ( reverse_complement_naive ) some good advice from CodeReview.SE to loop over data! 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When I asked the question, github.com/biopython/biopython/blob/master/Bio/Seq.py # L860 for str ( my_seq ) for str my_seq! Approach to speeding up Python work the primary id used to write sequences to.! Gives reverse complement str biopython reverse complement my_seq ) % slower than the naive code in the reverse complement each... Recall a personal gift sent to an employee in error where appropriate is! Coworkers to find and share the link here in World War II to! Earlier would give a truncated version of repr ( my_seq ) for str ( my_seq ) give a!