In case of problems, please mail me at rarnold kimlab. Pre-requisit: find a fast Internet connection and take some time off from other duties. Achtung Attention! Close all cygwin windows. Install [a]ll optional external modules, [n]one, or choose [i]nteractively? Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively? Do you want to run tests that require connection to servers across the internet. Don't be confused if error messages appear in the first place or the program seems to do nothing for a while Instructions for installing BioPerl 1.
Open a shell and type gcc. If you get an error then you must install XCode from here. Download BioPerl 1. Then follow the instructions below.
This is an interactive installation so if at some point, the installation prompts to download something from CPAN respond with yes. Reload to refresh your session. You signed out in another tab or window. You need at least the corresponding version of Bioperl. Since this. Installation instructions at the following address apply here:. The next 2 sections summarize the essential points from there.
To install using CPAN you will need a recent version v1. Find the name of the bioperl-run version you want:. If you've installed everything perfectly then you may pass all the tests. It's also possible that you may fail some tests. Until the organizations creating these databases agree on standard sets of names and formats all that Bioperl can do is do make reasonable choices.
Translation in bioinformatics can mean slightly different things, either translating a nucleotide sequence from start to end or translate the actual coding regions in mRNAs or cDNAs. The Bioperl implementation of sequence translation does both of these.
Any sequence object with an alphabet of dna or rna can be translated by simply using translate which returns a protein sequence object:.
All codons will be translated, including those before and after any initiation and termination codons. However, the translate method can also be passed several optional parameters to modify its behavior.
You can also determine the frame of the translation. The default frame starts at the first nucleotide frame 0. To get translation in the next frame we would write:. Specifically, translate needs to confirm that the open reading frame has appropriate start and terminator codons at the very beginning and the very end of the sequence and that there are no terminator codons present within the sequence in frame 0.
In addition, if the genetic code being used has an atypical non-ATG start codon, the translate method needs to convert the initial amino acid to methionine. If complete is set to true and the criteria for a proper CDS are not met, the method, by default, issues a warning. By setting throw to 1, one can instead instruct the program to die if an improper CDS is found, e. All these tables can be seen in Bio::Tools::CodonTable. For example, for mitochondrial translation:. You can also create a custom codon table and pass this to translate , the code will look something like this:.
See Bio::Tools::CodonTable for information on the format of a codon table. To tell translate to use only ATG or atg as the initiation codon set -start to atg :.
The -start argument only applies when -orf is set to 1. Last trick. When -complete is set to 1 this character is removed. So, with this:.
In addition to the methods directly available in the Seq object, Bioperl provides various helper objects to determine additional information about a sequence. For example, the Bio::Tools::SeqStats object provides methods for obtaining the molecular weight of the sequence as well the number of occurrences of each of the component residues bases for a nucleic acid or amino acids for a protein.
For nucleic acids, also returns counts of the number of codons used. For example:. Note: sometimes sequences will contain ambiguous codes. You have access to a large number of sequence analysis programs within Bioperl. Typically this means you have a means to run the program and frequently a means of parsing the resulting output, or report, as well. The example code assumes that you used the formatdb program to index the database sequence file db.
As usual, we start by choosing a module to use, in this case. You stipulate some blastall parameters used by the blastall program by using new. All the data in the report ends up in the report object, and you can access or print out the data in all sorts of ways.
Bioperl enables you to run a wide variety of bioinformatics programs but in order to do so, in most cases, you will need to install the accessory bioperl-run package. In addition there is no guarantee that there is a corresponding parser for the program that you wish to run, but parsers have been built for the most popular programs. You can find the bioperl-run package on the download page.
One of the under-appreciated features of Bioperl is its ability to index sequence files. The idea is that you would create some sequence file locally and create an index file for it that enables you to retrieve sequences from the sequence file. Why would you want to do this? Speed, for one. Retrieving sequences from local, indexed sequence files is much faster than using the module used above that retrieves from a remote database.
Flexibility is another reason. All these modules are scripted in a similar way: you first index one or more files, then retrieve sequences from the indices. This is essentially the same thing as the following in tcsh or csh:. You would execute this script in the directory containing the sequence. Then you would retrieve a sequence object like this:.
However, what if you wanted to retrieve using some other key, like 1CRA in the example above? Bio::DB::Fasta has some features that Bio::Index::Fasta lacks, one of the more useful ones is that it was built to handle very large sequences and can retrieve sub-sequences from genome-size sequences efficiently. Here is an example:. This script indexes the genome.
One can also specify what ids can be used as keys, just as in Bio::Index::Fasta. The interfaces for these parsers are all similar.
Here are some examples on how to use these modules. A parser for the ePCR program is also available. A sample skeleton script for parsing an ePCR report and using the data to annotate a genomic sequence might look like this:.
Note that a Seq object was used as input. A object can execute a query like:.
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