You might be using some Unix word processor, emacs or vi, for example or nano, very easy to use, but not found on all Unix machines unfortunately. Start to write your script by entering something like: emacs seqio. Well, not just a sequence, you will be creating a sequence object, since Bioperl is written in an object-oriented way. Why be object-oriented? The reason is that thinking in terms of modules or objects turns out to be the most flexible, and ultimately the simplest, way to deal with data as complex as biological data. Once you get over your initial skepticism, and have written a few scripts, you will find this idea of an object becoming a bit more natural.
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You might be using some Unix word processor, emacs or vi, for example or nano, very easy to use, but not found on all Unix machines unfortunately. Start to write your script by entering something like: emacs seqio.
Well, not just a sequence, you will be creating a sequence object, since Bioperl is written in an object-oriented way. Why be object-oriented?
The reason is that thinking in terms of modules or objects turns out to be the most flexible, and ultimately the simplest, way to deal with data as complex as biological data. Once you get over your initial skepticism, and have written a few scripts, you will find this idea of an object becoming a bit more natural. One way to think about an object in software is that it is a container for data.
The typical sequence entry contains different sorts of data a sequence, one or more identifiers, and so on so it will serve as a nice example of what an object can be. We will use this module to create a object. The module is one of the central modules in Bioperl. The analogous object, or Sequence object, or Seq object, is ubiquitous in Bioperl, it contains a single sequence and associated names, identifiers, and properties.
Note that the code tells Bioperl that the sequence is DNA the choices here are dna, rna, and protein , this is the wise thing to do. Any time you explicitly create an object, you will use this new method. In object-oriented programming the term method is used instead. The object was described as a data container, but it is more than that.
It can also do work, meaning it can use or call specific methods taken from the module or modules that were used to create it. For example, the Bio::Seq module can access a method named seq that will print out the sequence of objects.
You could use it like this:! You could say that this example shows how to pass arguments to the new method. Writing a sequence to a file This next example will show how two objects can work together to create a sequence file. By using in this manner you will be able to get input and make output for all of the sequence file formats supported by Bioperl the SeqIO HOWTO has a complete list of supported formats.
The -format argument, fasta, tells the object that it should create the file in fasta format. Another way to think about this is that we hand the Sequence object to the object since understands how to take information from the Sequence object and write to a file using that information, in this case in fasta format.
This is understandable in some respects. Using open immediately forces you to do the parsing of the sequence file and this can get complicated very quickly.
The syntax will look familiar:! In fact, the suffix fasta is one that SeqIO understands, so -format is unnecessary above. It may be useful to tell SeqIO the alphabet of the input, using the -alphabet argument. What this does is to tell SeqIO not to try to determine the alphabet dna, rna, protein.
There may also be odd characters present in the sequence that SeqIO objects to e. Set -alphabet to a value when reading sequences and SeqIO will not attempt to guess the alphabet of those sequences or validate the sequences.
Retrieving a sequence from a database One of the strengths of Bioperl is that it allows you to retrieve sequences from all sorts of sources, files, remote databases, local databases, regardless of their format. What will we retrieve? Again, a Sequence object. Make sure to use the proper identifier for the method you use, the methods are not interchangeable. Retrieving multiple sequences from a database There are more sophisticated ways to query Genbank than this.
Want all Arabidopsis topoisomerases from Genbank Nucleotide? Note This capability to query by string and field is only available for [GenBank as of Bioperl version 1. The idea is that you will use a stream whenever you expect to retrieve a stream or series of sequence objects. You can use the SLEN field to limit the size of the sequences you retrieve. The table below lists the methods available to you if you have a Sequence object in hand.
Some methods, such as seq , can be used to get or set values. Bear in mind that not all values, such as molecule or division, are found in all sequence formats, you have to know something about your input sequences in order to get some of these values.
BIOPERL TUTORIALS PDF
You are more than welcome to contribute your script! We encourage collaborative code, in particular in Perl. You can help us in many different ways, from just a simple statement about how you have used BioPerl to doing something interesting to contributing a whole new object hierarchy. Here are some ways of helping us: Asking questions and telling us you used it We are very interested to hear how you experienced using BioPerl.
Golkree No single individual owns the project, rather it is owned by the community of contributors. A Strategy pattern defines one or more operations that a particular implementation must support. PrimarySeq — Basic sequence operations aa and nt Bio:: A new generation of protein database search programs. Bioperl is a collection of more than Perl modules for bioinformatics that have been written and maintained by an international group of volunteers. This tutorial helps users extract DNA sequences of interest from a database using a BioPerl script by providing the example of extracting ubiquitin promoter sequences from a draft of the tomato genome sequence. PrimarySeqI Can be assured that at least these methods will be implemented by subclasses Can treat all inheriting objects as if they were the same, i.