Fast and sensitive protein sequence homology searches using hierarchical cluster BLAST

Abstract

19711 15 (Tel): (302) 831-3235 16 (Fax): (302) 831-4841 17 ABSTRACT 24The throughput of DNA sequencing continues to increase, allowing researchers 25 to analyze genomes of interest at greater depths. An unintended consequence of this 26 data deluge is the increased cost of analyzing these datasets. As a result, genome and 27 metagenome annotation pipelines are left with a few options: (i) search against smaller 28 reference databases, (ii) use faster, but less sensitive, algorithms to assess sequence 29 similarities, or (iii) invest in computing hardware specifically designed to improve BLAST 30 searches such as GPGPU systems and/or large CPU-rich clusters. 31We present a pipeline that improves the speed of amino acid sequence 32 homology searches with a minimal decrease in sensitivity and specificity by searching 33 against hierarchical clusters. Briefly, the pipeline requires two homology searches: the 34 first search is against a clustered version of the database and the second is against 35 sequences belonging to clusters with a hit from the first search. We tested this method 36 using two assembled viral metagenomes and three databases 37 Metagenomes Online, and UniRef100). Hierarchical cluster homology searching proved 38 to be 12-times faster than BLASTp and produced alignments that were nearly identical 39to BLASTp (precision=0.99; recall=0.97). This approach is ideal when searching large 40 collections of sequences against large databases. 41 42

Unveiling the mysteries: Functional insights into hypothetical proteins from Bacteroides fragilis 638R

“…This approach allows for the inference of protein structure, function, and evolution [ 33 ]. The goal of the homology search was to analyze the protein sequences and detect similarities that may not be evident from sequence alone, but can be inferred from protein spatial structures [ 34 ]. Sequences lacking identity with hypothetical proteins were selected for further analysis.…”