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webPRC / web Profile Comparer
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.
d-Omix
Integrates various analyses of domain combinations into a unified and comparative platform. d-Omix is applicable with various domain search tools. It provides five distinct sections: (1) Data tab for data submission and four services including (2) Tree tab for comparative protein evolution based on domain distances; (3) Graph tab for comparative domain combination based on domain graphs; (4) Alignment tab for comparative proteomes based on domain architecture alignments; (5) and Interaction tab for building a putative protein interaction network from domain–domain interactions (DDIs).
MetaDomain
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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