Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches | Zendy

Marianne M. Lee | Zendy; Michael K. Chan | Zendy; Ralf Bundschuh | Zendy

Open Access

Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches

Author(s) -

Marianne M. Lee,

Michael K. Chan,

Ralf Bundschuh

Publication year - 2008

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btn130

Subject(s) - false positive paradox , computer science , rank (graph theory) , discriminator , simple (philosophy) , true positive rate , set (abstract data type) , algorithm , data mining , artificial intelligence , pattern recognition (psychology) , detector , mathematics , combinatorics , programming language , telecommunications , philosophy , epistemology

The deluge of biological information from different genomic initiatives and the rapid advancement in biotechnologies have made bioinformatics tools an integral part of modern biology. Among the widely used sequence alignment tools, BLAST and PSI-BLAST are arguably the most popular. PSI-BLAST, which uses an iterative profile position specific score matrix (PSSM)-based search strategy, is more sensitive than BLAST in detecting weak homologies, thus making it suitable for remote homolog detection. Many refinements have been made to improve PSI-BLAST, and its computational efficiency and high specificity have been much touted. Nevertheless, corruption of its profile via the incorporation of false positive sequences remains a major challenge.

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