3.2.1 BLAST
BLAST is the most well-known analytics tool in life sciences and has
become an essential program in every branch of biology to find regions
of local similarity between biological (protein or nucleotide) sequences
(Altschul et al., 1997; Cock et al., 2009). While the web-based National
Center for Biotechnology Information (NCBI) BLAST suite of programs
provides comprehensive sequence comparison, it is a major bottleneck due
to delayed new data submission with embargo issues (including
user-specific new data) and public availability on central BLAST
repositories. Fortunately, BLAST can be installed and run locally, but
its usage can be challenging for biologists who have limited experience
of command-line interfaces. Furthermore, purchasing commercial software
of a rich GUI-standalone tool (e.g. CLC Genomic Workbench and Geneious)
and its licences is too expensive for many researchers and laboratories.
To resolve these matters, easyfm provides a new Python-based free
GUI for BLAST and more (Figure 2). Users can explore all BLAST+
(v2.11.0) features by creating a local database from which output format
can be selected for including controlling analyses parameters and CPU
cores. Even a common BLAST archive format (ASN.1) can be converted to
any BLAST output format via Result Convert (Figure 2D). To save storage
space and enable faster downstream analysis, a BLAST extensible markup
language (XML) format (even generated externally) can be converted into
a more compact form (e.g. a human-readable csv file) via XML Parsing
(Figure 2E). Along with recent free tools (Blanco-MÃguez., et al2018;
Kim et al., 2012; Priyam et al., 2019), easyfm BLAST enables easy
and seamless integration of visual and interactive representations of
BLAST outputs supporting sequence similarity search. In particular,easyfm offers support for creating/searching a local database,
changing format and parsing XML files as a standalone cross-platform
application. This comprehensive and autonomous interface makeseasyfm unique when compared to other free existing tools which
need to rely on several different web servers.