Multiple domain alignment software tools | Protein sequence data analysis
The best currently available methods to study domain arrangements are classical multiple sequence alignment (MSA) methods. However, these alignment methods usually do not explicitely take domain arrangements into account and therefore do not incorporate any restriction concerning their alignment.
Computes geometrical core of a family of protein 3D structures. Geometrical core is a web application that determines the subset of alignment positions those atoms are disposed similarly in all structures. Users can set various options of the computation including the desired distance threshold, the minimal core size as well as the maximum numbers of cores on the final output or the Bron-Kerbosch algorithm timeout.
Enables users of the CDD (conserved domain database) resource to examine curated hierarchies. CDD and CDTree used in concert, serve as a powerful tool in protein classification, as they allow users to analyze protein sequences in the context of domain family hierarchies.
Simplifies the utilization of Profile Comparer (PRC) for finding domains related to a query alignment. webPRC is designed to simplify the research for distant homologues or similar alignments in a number of domain databases. It supplies an additional functionality for hidden Markov models (HMM)-to-alignment translation. Moreover, users can view the domain annotation, evaluate the PRC hits with the Jalview multiple alignment editor and generate logos from the aligned HMMs or the aligned multiple alignments.
Provides a protein domain classification for short reads generated by next-generation sequencing technologies. MetaDomain uses relaxed position-specific score thresholds to align more reads to a profile HMM while using the distribution of alignment positions as an additional constraint to control false positive matches. It can achieve better sensitivity, in transcriptomic data of a bacterial genome and a soil metagenomic data set, than the state-of-the-art profile HMM alignment tool in identifying encoded domains from short sequences.
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