OAOD (UGENE)

Application: UGENE

What it is:

Unipro UGENE is a cross-platform visual environment for DNA and
protein sequence analysis. UGENE integrates the most important
bioinformatics computational algorithms and provides an easy-to-use
GUI for performing complex analysis of the genomic data. One of the
main features of UGENE is a designer for custom bioinformatics
workflows.

Features:

* Multiple sequence alignment using MUSCLE 3,4 and KAlign;
* HMM profiles build and search, based on the source of HMMER 2 and HMMER 3;
* PCR Primers design using Primer 3;
* Protein secondary structure prediction using GOR IV and PSIPRED;
* Phylogenetic analysis with Phylip;
* Search for restriction enzymes and integration with REBASE;
* Extremely fast repeat finder;
* DNA reference assembly using Bowtie;
* Search for transcription factor binding sites using SITECON;
* Protein back translation;
* ORF finder;
* Complete Smith-Waterman algorithm implementation;
* Comparing genomes using dotplot view.

To know more about:

http://ugene.unipro.ru/

To install in ubuntu:

sudo apt-get install ugene

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