MOTIVATION: Single-molecule, real-time sequencing (SMRT) developed by Pacific 
BioSciences produces longer reads than secondary generation sequencing 
technologies such as Illumina. The long read length enables PacBio sequencing to 
close gaps in genome assembly, reveal structural variations, and identify gene 
isoforms with higher accuracy in transcriptomic sequencing. However, PacBio data 
has high sequencing error rate and most of the errors are insertion or deletion 
errors. During alignment-based homology search, insertion or deletion errors in 
genes will cause frameshifts and may only lead to marginal alignment scores and 
short alignments. As a result, it is hard to distinguish true alignments from 
random alignments and the ambiguity will incur errors in structural and 
functional annotation. Existing frameshift correction tools are designed for 
data with much lower error rate and are not optimized for PacBio data. As an 
increasing number of groups are using SMRT, there is an urgent need for 
dedicated homology search tools for PacBio data.
RESULTS: In this work, we introduce Frame-Pro, a profile homology search tool 
for PacBio reads. Our tool corrects sequencing errors and also outputs the 
profile alignments of the corrected sequences against characterized protein 
families. We applied our tool to both simulated and real PacBio data. The 
results showed that our method enables more sensitive homology search, 
especially for PacBio data sets of low sequencing coverage. In addition, we can 
correct more errors when comparing with a popular error correction tool that 
does not rely on hybrid sequencing.
AVAILABILITY AND IMPLEMENTATION: The source code is freely available at 
https://sourceforge.net/projects/frame-pro/
CONTACT: yannisun@msu.edu.