Proteins are macromolecules essential for the structuring and functioning of living cells. Proteins generally have different functional regions which are conserved along evolution and are commonly termed as “functional motifs” or “domains”. Domains/motifs are found in different proteins and combinations and, as such, are functional protein subunits above the raw amino-acid level. Domain identification is thus an essential task in bioinformatics. Different strategies can be used to identify these regions of a target protein. Profile analysis, also known as sequence-profile comparison, is a powerful method. To identify new protein domains, an important database is used to compute a score that measures the similarity between the sequence and the domain. If the score is above a predefined threshold, the presence of the domain in the protein can be asserted. However this method may miss several domains when applied to an organism that is phylogenetically distant from the species used.
Permits to interactively visualize and analyse molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. UCSF Chimera allows users to incorporate new features. It contains some extensions which permits to visualize large-scale molecular assemblies such as viral coats, and allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions can be used for extend the tool capabilities.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
A generic tool for pairwise sequence comparison. Exonerate allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics. The Exonerate package comes with a selection of utilities for performing simple manipulations quickly on fasta files beyond 2Gb.
Allows automation improvement of gene structures in Arabidopsis thaliana. PASA was used in Eukaryotic genome annotation projects such as Rice, Aspergillus species, Plasmodium falciparum, Schistosoma mansoni, Aedes aegypti, mouse, human, among others. This tool is able to recognize and organize splicing variations supported by the transcript alignments. It can clean the transcripts, validate perfect alignments or procced to automatic genome annotation.
Offers a framework for processing commonly used biological data. BioJava consists of several independent modules built using Maven. The software contains state-of-the-art algorithms, several file parsers, and data models to perform various calculations and to facilitate working with the standard data formats. It enables application development and analysis.
Generates an hidden Markov model (HMM) from the alignments given and calculates the optimal alignment and all significant non-overlapping suboptimal alignments. HHalign compares two alignments with each other or, if only one alignment is entered, the alignment with itself. It is very sensitive and can detect very divergent repeats. The tool only accepts entire alignments and can’t build alignments automatically from a single sequence.