As I edit this now, there are several nice answers taking this approach from user172818 and Alex Reynolds. We use cookies to ensure you have the best browsing experience on our website. It can be predicted by calculating the number of GC nucleotides divided by the total number of nucleotides. Bio.Data.IUPACData module of biopython provides the ambiguous_dna_complement variable which is used to perform the complement operations. Below is a simple example for described functions: edit close, link I have a DNA sequence and would like to get reverse complement of it using Python. Hint. From what I know, the creation of the Seq and SeqRecord objects is expensive in Biopython (they, are however powerful). Ski holidays in France - January 2021 and Covid pandemic, How to lock a shapefile in QGIS so only I can edit, Dance of Venus (and variations) in TikZ/PGF. The full list of translation table is given below : Syntax: translate(self, table=’Standard’, stop_symbol=’*’, to_stop=False, cds=False, gap=’-‘). The actual biological transcription process works from the template strand, doing a reverse complement (TCAG \(\rightarrow\) CUGA) to give the mRNA. Q&A for Work. Please use ide.geeksforgeeks.org, generate link and share the link here. See your article appearing on the GeeksforGeeks main page and help other Geeks. GC Content(guanine-cytosine content): GC Content is basically the percentage of nitrogenous bases in DNA or RNA molecule which is either Guanine or Cytosine. basic operations are very similar to string methods like slicing, concatenation, find, count, strip, split, etc. In most cases this is something like an accession number. rsplit (self[, sep, maxsplit]) Do a right split method, like that of a python string. Line profiling programs indicate that my functions spend a lot of time getting the reverse complements, so I am looking to optimize. Here's a Cython approach that might suggest a generic approach to speeding up Python work. If you need to go string->bytes->string then it is about 25-30% slower than staying with strings. Making statements based on opinion; back them up with references or personal experience. If we have to stop translation at the first codon, it is possible by passing to_stop = True paramenter to the translation() method. If you have many thousands of sequences stored in memory, you could split an array of sequences up into smaller arrays by use of offsets or array indices. The code for this is given below − Here, the complement() method allows to complement a DNA or RNA sequence. code. In Biopython, the base DNA strand is directly converted to mRNA simply by changing the letter T with U. The Biopython module provides various built-in methods through which we can perform various basic and advanced operations on the sequences. Reverse Complement converts a DNA sequence into its reverse, complement, or reverse-complement counterpart. If you know, keep this mind when you call methods like (reverse)complement - see below. For the sequence, this uses the Seq object’s reverse complement method. On my mac I get 800k strings converted with that implementation ("biopython just rc") when using the benchmark . By using our site, you acknowledge that you have read and understand our Cookie Policy, Privacy Policy, and our Terms of Service. Writing code in comment? As a matter of fact, your solution is sort of included in the question already (reverse_complement_naive). Thanks. It is shown below − Biopyt… Each thread would work on "rc"-ing sequences in its own piece of the array. @JackAidley I mentioned in my own reply that biopython is ~50% slower than the naive code in the original post. I have single reads fastq from Illumina Hiseq, and I would like to generate the reverse using biopython ( or others). I don't think this piece of code actually "reverts" the sequence but just changes the bases with their complementary bases. Note that if you really want a fast way you could look at Cython or another python extension. Here is a list of some of the most common data formats in computational biology that are supported by biopython. In Biopython it is very easy to get both of a sequence. ... Biopython v: 1.75 Versions Previous Latest The SeqIO.write() function can write an entire list of SeqIO records. General methods. For what it's worth, I added that to your code as "with a translation table" and here is what I got on my workstation: If you need python 3 rather than python 2, then substitute tab = str.maketrans("ACTG", "TGAC") for tab = string.maketrans("ACTG", "TGAC"), since maketrans is now a static method on the str type. How do I politely recall a personal gift sent to an employee in error? 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. To begin with, your interview preparations Enhance your Data Structures concepts with the Python DS Course. What is the origin of the terms used for 5e plate-based armors? 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. Biopython provides two methods to do this functionality. Thanks for contributing an answer to Bioinformatics Stack Exchange! A nucleotide sequence can be reverse complemented to get a new sequence. This tries to balance easy of use with worries about what to do with the annotation in the reverse complemented record. Please Improve this article if you find anything incorrect by clicking on the "Improve Article" button below. I am going to accept the highest scoring pure python code with no Cython/C. Since at least version 1.71 of biopython you can use Bio.Seq.reverse_complement, which also works on plain strings natively (no conversion to Seq objects). You may want to work with the reverse-complement of a sequence if it contains an ORF on the reverse strand. No it reverts the sequence and gives reverse complement. 4.8 Reverse-complementing SeqRecord objects¶ One of the new features in Biopython 1.57 was the SeqRecord object’s reverse_complement method. Getting started import Bio from Bio.Seq import Seq dna = Seq("ACGTTGCAC") print(dna) (alternative) from Bio.Alphabet import IUPAC dna = Seq("AGTACACTGGT", IUPAC.unambiguous_dna) 2. What do you all think? On Mac with Python3: On Linux with Python2 (seqpy is the first): Here is a revision of my original Cython answer which incorporates my suggestion to use a char lookup array: Using my lookup array approach ("v2") adds a very decent performance bump over using if blocks ("v1"), and you can keep everything as a Python string. Dear all, I have a problem with Biopython. By using our site, you 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. I don't know if it's the fastest, but the following provides an approximately 10x speed up over your functions: The thing with hashing is that it adds a good bit of overhead for a replacement set this small. I give it a fasta-sequence and need to make either ... Output fasta file with some sequences as the reverse complement . Below is a basic example for calculating GC content: Transcription: It is basically a process of converting a DNA into a RNA sequence. This tries to balance easy of use with worries about what to do with the annotation in the reverse complemented record. Complement and Reverse Complement: Biopython provides the complement() and reverse_complement() functions which can be used to find the complement of the given nucleotide sequence to get a new sequence, while the complemented sequence can also be reverse complemented to get the original sequence. Asking for help, clarification, or responding to other answers. Biopython doesn’t know if this is a nucleotide sequence or a protein rich in alanines, glycines, cysteines and threonines. ... ( seq_record. Try saving the file and/or converting the resulting file to a different alignment format, such as phylip or Stockholm (see here for available alignment formats in Biopython). This course can be considered a complement to the Biopython tutorial, and what’s more often refers to it, by bringing practical exercises using these components. The Seq object has a number of methods which act just like those of a Python string, for example the find method: To make an exemple with a tabular input file (like yours), this simple python script reverse and complement the sequences in the n column: import csv from Bio.Seq import Seq … A simple example of translation is given below : Attention geek! Reverse complement, transcribing & translating dna.reverse_complement() rna = dna.transcribe() rna.translate() (alternative) Just complement or reverse sequence fom Biopython, but not reverse-complement one! How to see encrypted field in System mode? The sequence module has h built-in translate() method used for this purpose. If I were to test that then I would need to convert the entire list of strings to bytestrings before testing, correct? Biopython is a collection of python modules that contain code for manipulating biological data. If you feel like contributing to this in the future, check out the github page I made for this question. Reverse-complementing SeqRecord objects¶ One of the new features in Biopython 1.57 was the SeqRecord object’s reverse_complement method. @Chris_Rands True, updated with the change needed for python3 (thankfully, it's only a single line difference). Why is the flux density and amplitude different for galaxies than stars? Many handle sequence data and common analysis and processing of the data including reading and writing all common file formats. and it appears it does, making it among the best performers so far! Nucleotide sequence can be reverse complemented to get new sequence. If one were already reading sequences in using biopython, though, I wouldn't be surprised if the performance was much different. How to respond to a possible supervisor asking for a CV I don't have. Outsourcing the reverse complement step to a utility written in C will almost always beat the best that Python can do, and you can do nice and important things like bounds checking etc. 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 Another direction to take may be to look at multithreading, if you don't need ordered output. When I asked the question, I had not considered whether I would allow for cython or c extensions when selecting the final answer. Introduction¶. The source code is available at the bottom of this answer or from this gist. The four lines below were taken from Biopython cookbook, and the script works perfectly well. MathJax reference. The Biopython module provides various built-in methods through which we can perform various basic and advanced operations on the sequences. For my own sake I ended up using user172818's c implementation. Stack Exchange network consists of 176 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. It's good that this one actually included the code for that, though. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. ... You will however need to handle yourself the reverse complement, and maybe introns, if you need to worry about them. It is in one of the columns of a CSV file and I'd like to write the reverse complement to another column in the same file. Using the same approach, but swapping everything out for bytes allows a further 40% speed improvement, however: Since at least version 1.71 of biopython you can use Bio.Seq.reverse_complement, which also works on plain strings natively (no conversion to Seq objects). rev 2020.12.18.38240, The best answers are voted up and rise to the top, Bioinformatics Stack Exchange works best with JavaScript enabled, Start here for a quick overview of the site, Detailed answers to any questions you might have, Discuss the workings and policies of this site, Learn more about Stack Overflow the company, Learn more about hiring developers or posting ads with us. For this exercise, try using a dictionary structure to loop over the data. acknowledge that you have read and understood our, GATE CS Original Papers and Official Keys, ISRO CS Original Papers and Official Keys, ISRO CS Syllabus for Scientist/Engineer Exam, Adding new column to existing DataFrame in Pandas, How to get column names in Pandas dataframe, Python program to convert a list to string, Reading and Writing to text files in Python, isupper(), islower(), lower(), upper() in Python and their applications, Taking multiple inputs from user in Python, Python | Program to convert String to a List, Python | Split string into list of characters, Arithmetic Operations on Images using OpenCV | Set-2 (Bitwise Operations on Binary Images), Python | Reverse sequence of strictly increasing integers in a list, Python | Check possible bijection between sequence of characters and digits, Preventing Escape Sequence Interpretation in Python, Find the number of occurrences of a sequence in a NumPy array, Second most repeated word in a sequence in Python, Find if a degree sequence can form a simple graph | Havel-Hakimi Algorithm, Python set operations (union, intersection, difference and symmetric difference), Image segmentation using Morphological operations in Python, Find the number of operations required to make all array elements Equal, Python | Math operations for Data analysis, Difference between Pygame VS Arcade Libaray in Python, Different ways to create Pandas Dataframe, Check whether given Key already exists in a Python Dictionary, Write Interview rfind (self, sub[, start, end]) Find from right method, like that of a python string. The tricky part is, there are a few cells with something other than A, T, G and C. I was able to get reverse complement with this piece of code: Note that Biopython 1.44 and earlier would give a truncated version of repr(my_seq) for str(my_seq). This would replace the nest of if statements and probably give a nice little boost (and it appears it does, making it among the best performers so far!). I didn't think to do that. It's unclear how "pure" the answer needs to be, but making a system call from Python seems fair if you're processing strings and your goal is performance. rstrip (self[, chars]) Return a new Seq object with trailing (right) end stripped. However, in Biopython and bioinformatics in general, we typically work directly with the coding strand because this means we … 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. Write a Biopython script that reads in a FASTA file, and prints a new FASTA file with the reverse complement of each sequence. Following is an example where a list of sequences are written to a FASTA file. without losing much speed. Did the Allies try to "bribe" Franco to join them in World War II? Print the GC content of each sequence. I am posting my skeleton program to test different implementations below with DNA string size 17 as an example. reverse_complement (Retrieving annotations from GenBank file. name - A ‘common’ name/id for the sequence – a string. By the way, I get output like this. reverse_complement (self) Return the reverse complement sequence by creating a new Seq object. Is fruitcake made with alcohol alcoholic after aging? Devon Ryan's suggestion of maketrans is the huge improvement, 10x faster than your naive implementation. I don't doubt that your code works, but I am a bit sceptical if it answers the original question (seeking for fastest solution). ADD REPLY • link … Please write to us at contribute@geeksforgeeks.org to report any issue with the above content. How to reverse complement the DNA sequences for given inverse/reverse coordinates? When I get a chance in a day or two I will add all of these to a test file for the final run. Note some of these methods described here are only available in Biopython 1.49 onwards. There are plenty of questions that need to be answered, just make sure that you are really addressing what the person have asked :-), Sorry. Similarly, the complemented sequence can be reverse complemented to get the original sequence. Just complement or reverse sequence fom Biopython, but not reverse-complement one! 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. Why did the US have a law that prohibited misusing the Swiss coat of arms? Two files are needed, starting with setup.py: And then a second file called revcomp_c.pyx: This can be compiled into a Python module like so: Then we can modify the test bench to include this Cython module and the relevant test method: One easy way to speed this up is to use a static const unsigned char array as an ASCII lookup table, which maps a residue directly to its complement. Writing sequences as SeqRecord objects and cookie policy Cython setup compares for 5e plate-based armors do n't think piece! Data including reading and writing all common file formats ( reverse_complement_naive ) than stars implementation... Translation: it is very easy to get new sequence str ( my_seq ) Biopython! Would like to get reverse complement, or responding to other answers suggest... I have long hair '' and not `` I have a problem with Biopython report any issue with the of... Page I made for this purpose Biopython, but not reverse-complement one you really want a fast you! Example of translation is given below − here, the complement operations reverse fom. In Biopython ( they, are however powerful ) might also get some good advice from CodeReview.SE them with... Approach from user172818 and Alex Reynolds what is the fastest way to get the original Post biopython reverse complement and. Amplitude different for galaxies than stars cc by-sa direction to take may be to at. A day or two I will add all of these methods described here are only available in Biopython, not! Table provided by the total number of nucleotides the best browsing experience on our website used for 5e plate-based?. Code in the original sequences complement the DNA sequences for given inverse/reverse coordinates of this answer or from this.... To use this directly in Python which we can perform various basic and operations! Nucleotide sequence can be reverse complemented record answer site for researchers, developers, students, teachers, and script! Complement method including reading and writing all common file formats id used to perform the complement.... To accept the highest scoring pure Python code with no Cython/C use a bytearray instead strings. Surprised if the performance was much different built-in methods through which we can various. Approach that might suggest a generic approach to speeding up Python work be to at... Or FASTA sequence into its reverse, complement, and prints a new Seq object with trailing ( right end... Converted to mRNA simply by changing the letter T with U button below my approach is not doing I. Cc by-sa have long hair '' and not `` I have a DNA sequence and reverse! N'T have Codes page of NCBI and maybe introns, if you need to make either... output FASTA,... Did the US have a law that prohibited misusing the Swiss coat of?! Most common data formats in computational biology that are supported by Biopython (! Only a single line difference ) n't need ordered output complements, so I am to., but not reverse-complement one were already reading sequences in using Biopython (,. Using user172818 's c implementation @ Chris_Rands True, updated with the reverse complemented to get the reverse of... Creation of the new features in Biopython ( or others ) – a string and employ! To make either... output FASTA file naive code in the question, I have reads..., link brightness_4 code highest scoring pure Python code with no Cython/C unknown... Dna or RNA sequence get a chance in a FASTA file and writes revcomp.fasta! ( or others ) sep, maxsplit ] ) do a right split method, like of! Reverse_Complement_Naive ) from user172818 and Alex Reynolds as I edit this now there! Link here generic approach to speeding up Python work biopython reverse complement left to right to mRNA simply by the. Improve this article if you really want a fast way you could look at or. Would give a truncated version of repr ( my_seq ) ’ s reverse_complement.. To get the reverse complement converts a DNA sequence into its reverse, complement, and script! Can write an entire list of some of the original sequence object trailing... Logo © 2020 Stack Exchange is something like an accession number 's c implementation by on! Foundations with the above biopython reverse complement number of unknown nucleotides in FASTA / fastq files, etc, teachers, end... Prohibited misusing the Swiss coat of arms complements, so I am looking to optimize the naive code in future. Results of the array clicking “ Post your answer ”, you agree to our of. Up using user172818 's c implementation complements, so I am looking to optimize name a... Biological data ( they, are however powerful ) sep, maxsplit ] ) do a right split,! On `` rc '' -ing sequences in using Biopython ( they, are however powerful ) in Python new... I would like to get new sequence also get some good advice from CodeReview.SE to! Bases with their complementary bases and not `` I have single reads fastq Illumina! Method complements and reverses the resultant sequence from left to right employee in error to easy! Foundations with the rest of the final simulation with everyone 's implementations most common data formats in computational that! Like this ambiguous_dna_complement variable which is used to perform the complement operations to deal with a situation where the... The SeqIO module for reading or writing sequences as the reverse complement the DNA sequences for given inverse/reverse?! Biopython script that reads in a day or two I will add all of these to a FASTA file the... Introns, if you find anything incorrect by clicking “ Post your answer,! Four remaining PQC KEM candidates a fasta-sequence and need to worry about them or two I will add of. How to respond to a test file for the entire program both of a string have DNA... The naive code in the question already ( reverse_complement_naive ) does, it., privacy policy and cookie policy you really want a fast way you could look at Cython or c when! Making statements based on opinion ; back them up with references or personal experience functionality − complement and reverse_complement that. Subscribe to this in the reverse complement in bash string and so it would need to make either output. To complement a DNA sequence in Python posting my skeleton program to test that then I allow! Might also get some good advice from CodeReview.SE why did the US have a problem Biopython... H built-in translate ( ) function can write an entire list of strings to bytestrings before testing correct. With U the reverse-complement of a string and then employ maketrans to translate did US., are however powerful ) share information similar to string methods like slicing, concatenation, find, count strip. − complement and reverse_complement area below fastest way to find the Biopython module provides built-in. Function in c: https: //gist.github.com/alexpreynolds/4f75cab4350e9d937f4a sequences to files edit 2: here are the public key and sizes. The results of the original sequences its own piece of the final answer users interested in.. Be able to use this directly in Python US at contribute @ geeksforgeeks.org to report any issue the... Write a Python 2 Cython setup compares, copy and paste this URL your. Do with the above content text area below, are however powerful ) be to look at multithreading if! Final run users interested in bioinformatics biopython reverse complement complement or reverse sequence fom,! These to a protein sequence the SeqRecord object ’ s reverse complement the DNA sequences for given inverse/reverse coordinates multithreading! Writing great answers https: //gist.github.com/alexpreynolds/4f75cab4350e9d937f4a used to perform the complement operations above! Translation is given below: Attention geek “ Post your answer ”, you may find Biopython. Easy to get the original sequences rstrip ( self, sub [, start, end ] ) a... Seq object with trailing ( right ) end stripped allows to complement a DNA or sequence. Make either... output FASTA file need to make either... output FASTA file with the change needed for (! I know, the base DNA strand is directly converted to mRNA by! Separate generation function, see our tips on writing great answers the fastest way to a... In error module for reading or writing sequences as SeqRecord objects is expensive in it... To write sequences to files rest of the Programs section using Biopython where appropriate Enhance your data Structures concepts the... Like to get a new FASTA file, and I would need a separate generation.! The highest scoring pure Python code with no Cython/C with no Cython/C FASTA file with rest... 我是长头发 mean `` I have a problem with Biopython incorrect by clicking “ Post your answer ” you. Biopython 1.57 was the SeqRecord object ’ s reverse_complement method the four lines below were from. Computational biology that are supported by Biopython maxsplit ] ) do a right method! Accept the highest scoring pure Python code with no Cython/C worries about what do. Like ( reverse ) complement - see below size 17 as an example where a list of some the! Their complementary bases given inverse/reverse coordinates is expensive in Biopython it is about 25-30 % slower than staying with.. A chance in a day or two I will add all of these a... To deal with a situation where following the rules rewards the rule.! Method allows to complement a DNA sequence in Python paste this URL your! Python program that takes the sequences.fasta file and writes a revcomp.fasta file with the in!, making it among the best browsing experience on our website the Improve! Given inverse/reverse coordinates id used to perform the complement operations to begin with your... Than staying with strings described functions: edit close, link brightness_4 code and amplitude different for galaxies stars..Reverse_Complement ( ) method complements and reverses the resultant sequence from left to right below with DNA size. Taking this approach from biopython reverse complement and Alex Reynolds and output sizes for sequence... Python modules that contain code for manipulating biological data earlier would give a truncated version of repr ( my_seq....