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CompositeSearch
Detects composite gene families in large data sets. CompositeSearch is a program allowing identification of composite gene families in the range of several million sequences. This tool assists users in the investigation of the process of gene remodeling in large data sets, for example metagenomes and thousands of complete genomes. It provides descriptions regarding the distribution and primary sequence conservation of gene families, permitting critical biological analyses of data.
PANADA / Protein Association Network Annotation Determination and Analysis
Generates protein similarity networks to be used with Cytoscape. PANADA allows the user to either automatically search similar sequences or to generate a network with a set of selected proteins. The similarity networks can be used for the visual analysis of similarity relationships among sequences or to assess functional annotation inferred from homology. PANADA complements other more traditional tools such as phylogenetic trees and multiple sequence alignments, making use of the user's visual skills to identify patterns that allow the inference of novel properties. The main advantages consist in the automatic search and annotation of proteins with gene ontology (GO) terms from the database and the ability to choose two different approaches to prune the network topology. This produces networks that only contain edges for those pairwise comparisons that represent the highest similarities above a given threshold.
EFI-EST / Enzyme Function Initiative-Enzyme Similarity Tool
Facilitates analysis of sequence function space in enzyme families using sequence similarity networks (SSNs). EFI-EST is a web-server that generates SSNs in a predominately automated manner. The software allows users to explore local sequence-function space defined by a user-specified sequence and to generate the SSN for any Pfam or InterPro entry. It can be used to analyze sequence-function space in a functionally diverse enzyme superfamily.
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