Bioinformatics
- 1. Softwares
- 2. Free software • Free software is software that comes with permission for anyone to use, copy, and distribute, either verbatim or with modifications, either gratis or for a fee. In particular, this means that source code must be available. “If it's not source, it's not software.” • Free software is a matter of freedom, not price. • But proprietary software companies sometimes use the term “free software” to refer to price. • Sometimes they mean that you can obtain a binary copy at no charge; sometimes they mean that a copy is bundled with a computer that you are buying, and the price includes both.
- 3. Open Source software • The term “open source” software is used by some people to mean more or less the same category as free software. • It is not exactly the same class of software: they accept some licenses that is considered too restrictive, and there are free software licenses they have not accepted. • However, the differences in extension of the category are small: nearly all free software is open source, and nearly all open source software is free.
- 4. Public domain software • Public domain software is software that is not copyrighted. If the source code is in the public domain, that is a special case of non- copylefted free software, which means that some copies or modified versions may not be free at all. • In some cases, an executable program can be in the public domain but the source code is not available. This is not free software, because free software requires accessibility of source code. • Meanwhile, most free software is not in the public domain; it is copyrighted, and the copyright holders have legally given permission for everyone to use it in freedom, using a free software license. • Sometimes people use the term “public domain” in a loose fashion to mean “free” or “available gratis.” However, “public domain” is a legal term and means, precisely, “not copyrighted”.
- 5. Proprietary software • Proprietary software is software that is not free or semi-free. • Its use, redistribution or modification is prohibited, or requires you to ask for permission, or is restricted so much that you effectively can't do it freely. • The Free Software Foundation follows the rule that it cannot install any proprietary program on our computers except temporarily for the specific purpose of writing a free replacement for that very program.
- 6. • Freeware – The term “freeware” has no clear accepted definition, but it is commonly used for packages which permit redistribution but not modification (and their source code is not available). These packages are not free software, so please don't use “freeware” to refer to free software. • Shareware – Shareware is software which comes with permission for people to redistribute copies, but says that anyone who continues to use a copy is required to pay a license fee. Shareware is not free software, or even semi-free. There are two reasons it is not: • For most shareware, source code is not available; thus, you cannot modify the program at all. • Shareware does not come with permission to make a copy and install it without paying a license fee, not even for individuals engaging in nonprofit activity. (In practice, people often disregard the distribution terms and do this anyway, but the terms don't permit it.)
- 7. Commercial Software • Commercial software is software being developed by a business which aims to make money from the use of the software. • “Commercial” and “proprietary” are not the same thing! Most commercial software is proprietary, but there is commercial free software, and there is non-commercial non-free software. • For example, GNU Ada is developed by a company. It is always distributed under the terms of the GNU GPL, and every copy is free software; but its developers sell support contracts. When their salesmen speak to prospective customers, sometimes the customers say, “We would feel safer with a commercial compiler.” The salesmen reply, “GNU Ada is a commercial compiler; it happens to be free software.” • For the GNU Project, the emphasis is in the other order: the important thing is that GNU Ada is free software; whether it is commercial is just a detail. However, the additional development of GNU Ada that results from its being commercial is definitely beneficial.
- 8. EMBOSS - Bioinformatic analysis package
- 9. EMBOSS • EMBOSS is an acronym for European Molecular Biology Open Software Suite. • EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community • Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit.
- 10. Features • A properly constructed toolkit for creating robust bioinformatics applications or workflows. • A comprehensive set of sequence analysis programs. • Many sequence and structural formats are handled. • Extensive programming library for common sequence analysis tasks. • Additional programming libraries for many other areas including string handling, pattern-matching, list processing and database indexing. • It is free-of-charge.
- 11. • It is an open-source project. • It runs on practically UNIX MS Windows and MacOS. • Each application has the same style of interface so master one and you've mastered them all. • Has consistent user interface facility - GUI. • It integrates other popular publicly available packages. • It is free of arbitrary size limits: there are no limits on the amount of data that can be processed. • A major new version of EMBOSS is released each year.
- 12. • Popular applications include: • Prophet - Gapped alignment for profiles. • Infoseq - Displays some simple information about sequences. • Water - Smith-Waterman local alignment. • Pepstats - Protein statistics.showfeat Show features of a sequence. • Palindrome - Looks for inverted repeats in a nucleotide sequence. • Eprimer3 - Picks PCR primers and hybridization oligos. • Profit - Scan a sequence or database with a matrix or profile. • Extractseq - Extract regions from a sequence. • Marscan - Finds MAR/SAR sites in nucleic sequences. • Tfscan - Scans DNA sequences for transcription factors. • Patmatmotifs - Compares a protein sequence to the PROSITE motif database. • Showdb - Displays information on the currently available databases. • Wossname - Finds programs by keywords in their one-line documentation. • Abiview - Reads ABI file and display the trace. • Tranalign - Align nucleic coding regions given the aligned proteins. Applications in EMBOSS
- 13. EMBOSS Interfaces • An interface is something that comes between you and the raw horror of any computer's operating system. • An EMBOSS interface provides access to the applications and their options, including their input and output files. • EMBOSS is designed to make it relatively easy to automate the process of defining interface to the applications. • This includes graphical user interfaces (GUI) which are controlled with a mouse, for example to set options. • EMBOSS may also be interfaced via perl and python script modules, making it easier to run the programs and process the results.
- 14. Jemboss • Jemboss is a java based interface to EMBOSS. It provides the advantage of being able to provide sensible EMBOSS defaults on-the-fly for a given sequence or for a given input parameter. • Jemboss can run the EMBOSS applications interactively or as a batch process. The progress of the batch processes are monitored by a job manager. • Jemboss can be set up to work with a local EMBOSS installation or one installed on a remote server. Jemboss provides file managers for data transfer between the local machine and the remote machine that runs the EMBOSS applications. Local and remote files can be used in Jemboss. • There is also a project manager responsible for maintaining the details of each run and the input and output files. These can be called up at any time and deleted by the user. The user can also add notes for each run. • Jemboss is part of the EMBOSS distribution. This means that sites can download the code and set up Jemboss locally using a script.