Detection of new protein domains using co-occurrence: application to Plasmodium falciparum

Detection of Plasmodium falciparum Directly from Blood Samples Using the Polymerase Chain Reaction

Genetic Diversity Block 2 of Surface Protein-1 in Plasmodium Falciparum Merozoite by Nested-PCR Method in Southeastern Iran

Abstract       Background and Objectives: Plasmodium falciparum merozoite surface protein-1 (PfMSP-1) is a promising vaccine against malaria during its blood stages which play an important role in immunity to this disease. Polymorphic nature of this gene is a major obstacle in making an effective vaccine against malaria. In this study, the genetic diversity of Plasmodi...

A genomic perspective of protein kinases in Plasmodium falciparum.

Protein kinases are central to regulation of cellular signaling in the eukaryotes. Well-conserved and lineage-specific protein kinases have previously been identified from various completely sequenced genomes of eukaryotes. The current work describes a genome-wide analysis for protein kinases encoded in the Plasmodium falciparum genome. Using a few different profile matching methods, we have id...

Identification of Divergent Protein Domains by Combining HMM-HMM Comparisons and Co-Occurrence Detection

Identification of protein domains is a key step for understanding protein function. Hidden Markov Models (HMMs) have proved to be a powerful tool for this task. The Pfam database notably provides a large collection of HMMs which are widely used for the annotation of proteins in sequenced organisms. This is done via sequence/HMM comparisons. However, this approach may lack sensitivity when searc...

Improving pairwise comparison of protein sequences with domain co-occurrence

Comparing and aligning protein sequences is an essential task in bioinformatics. 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. However, to limit the number of false positives, these tools are used with stringent sequence-similarity thresholds and hence can miss...