3.2.2 BLAT
BLAT is one of the alignment algorithms developed for the pairwise
analysis and comparison of biological sequences with the primary goal of
inferring homology to discover the biological function of genomic
sequences (Kent, 2002). While BLAT is less sensitive than BLAST, BLAT
has a few clear advantages over BLAST from a practical standpoint in
speed and convenience (Bhagwat et al., 2012). Compared to pre-existing
pairwise sequence alignment tools, BLAT performed ~500
times faster with mRNA/DNA alignments and ~50 times
faster with protein/protein alignments (Kent, 2002). BLAT can be used
either as a web-based server-client program
(https://genome.ucsc.edu/cgi-bin/hgBlat) or as a standalone
command-line program (Bhagwat et al., 2012), but not a user-friendly
GUI. However, easyfm BLAT (v3.2.1) enables users to control all
parameters with a simple mouse click (Figure 3A) that can be a great
advantage for novice biologists. Along with freely availableeasyfm BLAST, easyfm BLAT will simplify distributed
computation pipelines to facilitate the rapid discovery of sequence
similarities between NGS datasets. However, if the target genome and
input sequences are big, using the standalone command-line BLAT in HPC
is more suitable for batch runs, and more efficient than the web- and
GUI-based BLAT because the standalone command-line in HPC can store more
memory.