Installing BLAST and ClustalW
In this chapter, you will learn how to install small programs. As examples, we are using BLAST. (Basic Local Alignment Search Tool) and ClustalW. BLAST is a powerful tool to find sequences in a database. ClustalW is a general purpose multiple sequence ali
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Installing BLAST and ClustalW
In this chapter, you will learn how to install small programs. As examples, we are using BLAST (Altschul et al. 1990) (Basic Local Alignment Search Tool) and ClustalW (Thompson et al. 1994). BLAST is a powerful tool to find sequences in a database. Assume you have sequenced a gene and now want to check whether there are already similar genes sequenced by somebody else. Then you “blast” your sequence against an online database and get similar sequences, if present, as an output. Now assume you have found 10 similar genes. Of course, you would like to find regions of high similarity, that is, regions where these genes are conserved. For this, one uses ClustalW. ClustalW is a general-purpose multiple-sequence alignment program for DNA or protein sequences. It produces biologically meaningful multiple-sequence alignments of divergent sequences. ClustalW calculates the best match for the selected sequences and lines them up such that the identities, similarities, and differences can be seen. Then evolutionary relationships can be visualized by generating cladograms or phylograms. Both programs use different installation procedures. BLAST comes as a packed and compressed archive that needs only to be unpacked. ClustalW comes as a packed and compressed archive, too. However, before you can run the program it needs to be compiled. This means you get the source code of the program and must create the executable files from it. I omit in this chapter the installation of BLAST+ and the use of modern (but black box) installation procedures. Both are explained in Sect. 4.1.2.5 at page 43.
9.1 Downloading the Programs via FTP First of all you need to download the programs and save them in your home directory. How does this work? Well, of course, it is necessary that your computer is connected to the Internet! I assume that it is working for you.
R. Wünschiers, Computational Biology, DOI: 10.1007/978-3-642-34749-8_9, © Springer-Verlag Berlin Heidelberg 2013
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9 Installing BLAST and ClustalW
Whenever you download a program you basically transfer data via the internet. This means you connect to a remote computer, copy a file to your computer, and finally disconnect from the remote computer. There is a special program for this: FTP. FTP is the user interface to the Internet standard f ile transfer protocol, which was especially designed for file transfer via the Internet. The program allows a user to transfer files to and from a remote network site. In fact, it is a very powerful program with many options. We will use only a small fraction of its capabilities. If you wish, take a look at the manual pages (man ftp).
9.1.1 Downloading BLAST We will not download the newest version of BLAST, which is at the time of writing these lines version 2.2.26, but version 2.2.4. This version has less dependencies than the newer ones and should run on all typical Linux installations. Now, let us start. Go into your home directory by typing cd (remember: using the command cd without any directory name wil
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