Boitechnology

BLAST is one of the most widely used bioinformatics programs[2], because it addresses a fundamental problem and the algorithm emphasizes speed over sensitivity. This emphasis on speed is vital to making the algorithm practical on the huge genome databases currently available, although subsequent algorithms can be even faster.

Before fast algorithms such as BLAST and FASTA were developed, doing database searches for the protein or nucleic sequences was very time consuming by using a full alignment program like dynamic programming. BLAST is about 50 times faster than dynamic programming; however, it cannot guarantee the optimal alignments of the query and database sequences as in the dynamic programming, but just works to find the related sequences in a database search. BLAST is more time efficient than FASTA by searching only for the more significant patterns in the sequences, but with comparative sensitivity. This could be further realized by knowing the algorithm of BLAST introduced below.

Examples of other questions that researchers use BLAST to answer are:
Which bacterial species have a protein that is related in lineage to a certain protein with known amino-acid sequence?
Where does a certain sequence of DNA originate?
What other genes encode proteins that exhibit structures or motifs such as ones that have just been determined?

BLAST is also often used as part of other algorithms that require approximate sequence matching.

The BLAST algorithm and the computer program that implements it were developed by Stephen Altschul, Warren Gish, David Lipman at the U.S. National Center for Biotechnology Information (NCBI), Webb Miller at the Pennsylvania State University, and Gene Myers at the University of Arizona. It is available on the web on the NCBI website. Alternative implementations include WU-BLAST and FSA-BLAST.

The original paper by Altschul, et al.[1] was the most highly cited paper published in the 1990s.[3]

In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold. For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence. The BLAST program was designed by Eugene Myers, Stephen Altschul, Warren Gish, David J. Lipman and Webb Miller at the NIH and was published in J. Mol. Biol. in 1990[1]

Arlequin is a free population genetics software. It performs several types of tests and calculations, including Fst, Hardy-Weinberg equilibrium, linkage disequilibrium, mismatch distribution, and pairwise difference tests.

It is currently in version 3.11 and is only available for Windows, though the previous version is still available for Windows, Mac OS X PPC, and Linu

Affymetrix GeneChip Operating Software (GCOS) is a software system for managing Affymetrix microarray data. It captures and analyzes the array images, provides workflow tracking of data, manages experiment dkkata, and carries out basic expression analysis.

ANGIS is deeply involved in post-graduate training courses and workshops. General Bioinformatic application workshops, along with specialist workshops in proteomics, microarray, database searching and phylogenetics are held in Sydney and elsewhere in the country. In-house training courses in these areas can be arranged, ranging in length from 1 - 4 days.

A large number of university departments have and are using BioManager as an undergraduate training tool. Academic subscriptions also include teaching logins for students use

ANGIS began as a project at the University of Sydney in 1990, originally the Sydney University Sequence Analysis Interface (SUSAI) as a multi-disciplinary effort spearheaded by Trevor Cole, Alex Reisner and Peter Reeves. One year later in 1991, SUSAI became ANGIS through the formation of the Australian Genomic Information Center (AGIC), a government sanctioned research center. ANGIS is currently operated by the University of Sydney in New South Wales, Australia within the newly formed Sydney Bioinformatics.

BioManager is the main resource ANGIS provides. BioManager was developed from the earlier tool BioNavigator which was originally developed by a now defunct Australian bioinformatics company, Entigen(1)[citation needed] BioManager is a subscription based system that allows for integration of multiplte bioinformatic computer packages to be used in a single web user interface. Data from analyses can be stored on the system or used as inputs to other packages in BioManager. ANGIS also provides a variety of training resources and courses to help make these tools readily usable by the scientific community. BioManager access is available to the Australian and New Zealand academic communities. Access from outside Australia and NZ is by enquiry. In March 2007, ANGIS is now overseen by the University of Sydney Centre, Sydney Bioinformatics.

The Australian National Genomic Information Service (ANGIS) provides access for biologists to a comprehensive system of bioinformatics software, databases, documentation, training and support, on a subscription basis. Whilst clearly targeted at Australian researchers, the tools ANGIS provides are available online and is available to investigators worldwide.

This program accepts sequences in FASTA format.

The output format includes: FASTA format, Clustal.