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.