![]() Received: ApAccepted: NovemPublished: January 2, 2018Ĭopyright: © 2018 Menichelli et al. falciparum, our approach allows identifying 2240 new domains for which, in most cases, no domain of the Pfam database could be linked.Ĭitation: Menichelli C, Gascuel O, Bréhélin L (2018) Improving pairwise comparison of protein sequences with domain co-occurrence. ![]() This approach makes use of the fact that protein domains tend to appear with a limited number of other domains on the same protein (the domain co-occurrence property). We propose here an approach to increase the sensitivity of pairwise sequence comparisons. However these approaches sometimes miss several hits, especially for species that are phylogenetically distant from reference organisms. One common approach for identifying the domains of a protein is to run sequence-sequence comparisons with local alignment tools as BLAST. Protein domains are sequential motifs that are conserved along evolution and are found in different proteins and in different combinations. Because they provide strong clues regarding protein functions, domains occupy a key position among the relevant annotations that can be assigned to a protein. Source code of the proposed approach and supplementary data are available at: ĭeciphering the functions of the different proteins of an organism constitutes a first step toward the understanding of its biology. Moreover, our study of the quality of the new domains in terms of alignment and physicochemical properties show that they are close to that of standard Pfam domains. Our method identified 2240 new domains for which, in most cases, no model of the Pfam database could be linked. The experimental findings showed an increase of 14% of the number of significant BLAST hits and an increase of 25% of the proteome area that can be covered with a domain. We used Plasmodium falciparum as a case study to evaluate our method. We propose a method to take this information into account in a typical BLAST analysis and to construct new domain families on the basis of these results. Domain co-occurrence is a strong feature of proteins, since most protein domains tend to appear with a limited number of other domains on the same protein. Here, we propose to use domain co-occurrence to increase the sensitivity of pairwise sequence comparisons. A solution to this problem is then to integrate additional contextual information to the procedure. However, to limit the number of false positives, these tools are used with stringent sequence-similarity thresholds and hence can miss several hits, especially for species that are phylogenetically distant from reference organisms. More specifically, local alignment tools like BLAST are widely used for identifying conserved protein sub-sequences, which likely correspond to protein domains or functional motifs. Comparing and aligning protein sequences is an essential task in bioinformatics.
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