Introduction to Bioinformatics
Introduction to MATLAB
Introduction to Biological data and their Physical, chemical and
Biological Properties.
Introduction to BI Toolbox of MATLAB.
Introduction to SEQtool list of Function under SEQtool.
Conclusion
INTRODUCTION TO BIOINFORMATI:-
During the last ten years, molecular biology has witnessed an
information revolution as a result both of the development of rapid DNA
sequencing techniques and of the corresponding progress in computer
based technologies which are allowing us to manage with this
information overflow in increasingly efficient ways. The broad term that
was coined in the mid 1980s to include computer applications in
biological sciences is Bioinformatics. The bioinformatics the term can
be considered to mean information technology applied to the
management and analysis of biological data.
This has some implications in diverse areas, ranging from
artificial intelligence and robotics to genome analysis.
BIOINFORMATICS DEFINITION
Algorithm development
Handle Graphics.
This is the MATLAB graphics system. It includes high-level commands
for two-dimensional and three-dimensional data visualization, image
processing, animation, and presentation graphics. It also includes low-
level commands that allow you to fully customize the appearance of
graphics as well as to build complete Graphical User Interfaces on your
MATLAB applications.
The MATLAB mathematical function library.
This is a vast collection of computational algorithms ranging from
elementary functions like sum, sine, cosine, and complex arithmetic, to
more sophisticated functions like matrix inverse, matrix eigenvalues,
Bessel functions, and fast Fourier transforms.
MATLAB helps you take your ideas beyond the desktop. You can run
your analyses on larger data sets and scale up to clusters and clouds.
MATLAB code can be integrated with other languages, enabling you to
deploy algorithms and applications within web, enterprise, and
production systems.
Biological Data And Their Physical Chemical And Biological
Properties:-
Each file format has been designed for specific needs and outputs in
mind.
GFF
VCF
FASTA The FASTA file format, for sequence data. Sometimes also
given as FNA or FAA (Fasta Nucleic Acid or Fasta Amino Acid).
FASTQ The FASTQ file format, for sequence data with quality.
Sometimes also given as QUAL.
Getting Started
High-Throughput Sequencing
Microarray Analysis
Sequence Analysis
Structural Analysis
Miscellaneous tools.
Iiiii Bioinformatics is done with sequence search programs like
BLAST, sequence analysis programs, like the EMBOSS and Staden
packages, structure prediction programs like THREADER or PHD or
molecular imaging/modelling programs like RasMol and WHATIF.
BLAST:
BLAST (Basic Local Alignment Search Tool) comes under the
category of homology and similarity tools. It is a set of search programs
designed for the Windows platform and is used to perform fast similarity
searches regardless of whether the query is for protein or DNA.
Comparison of nucleotide sequences in a database can be performed.
Also a protein database can be searched to find a match against the
queried protein sequence. NCBI has also introduced the new queuing
system to BLAST (Q BLAST) that allows users to retrieve results at their
convenience and format their results multiple times with different
formatting options.
INTRODUCTION TO SEQTOOL LIST OF FUNCTION UNDER SEQTOOL
1. 1.1 about seqtools
1. 1.1.1 special features
2. 1.1.2 user interaction
2. 1.2 seqtools help sources
3. 1.3 about registration and licenses
4. 1.4 user interaction (update policy)
5. 1.5 support (bug reports)
SEQtools does not come with a printed manual. As the whole SEQtools
organisation consists of a single person it is simply not possibly to
maintain the code, the context sensitive help and the web help. Although
I try to keep the context sensitive help which is build into the program
up-to date, the updating usually lags several revisions behind. Pressing
F1 brings up context sensitive help information relating to the currently
active program item.
You can access the SEQtools registration form either from the program
as shown below or by visiting www.seqtools.dk
Providing SEQtools to users free of charge has the dual advantage that
users all over the world get free access to a fairly comprehensive
software package for sequence handling and analysis. In return I get
information about bugs and receive useful user input in the form of
suggestions and comments from a large number of users.
The difficult economic situation of many students and scientist in third
world countries is an additional argument for making the use of
SEQtools free of charge. The only condition for the free access to
SEQtools is that users are requested to register after a testing period of
60 days and there after to keep their registration alive by renewing their
license every 60 days.
The user name and the registration key is entered in the form shown
below. Note that this information must be entered exactly as in the
license agreement. The user name is case and "space" sensitive.
Entering incorrect information will terminate SEQtools immediately.
You can extended your license atwww.seqtools.dkor by sending
anemail to me.
Seqtools has evolved in close association with its users. Numerous users
have contributed significantly to the program by suggesting new
functions to be included in the suite and - not least - by testing functions
and reporting the result to the author.