Biomedical Engineering Reference
In-Depth Information
3.2
Program Output
FastPCR automatically generates results at a third text editor,
“Result report,” in tabulated format for transferring to spreadsheet
software from the clipboard using copy-paste. Output results are
easy to save as Excel worksheet (.xls) or as Rich Text Format (.rtf)
text files, compatible with MS Excel or Open Office. The separated
output of the primer design is a list of primers, a set of primer pair
sequences with their theoretical PCR products, and, for multiplex
PCR, the result of the calculation of multiple-PCR primers for
given target sequences. In addition, the output shows optimal
annealing temperature for each primer pair, the size of PCR
product, and complete information for each designed primer and
for each multiplex PCR product set.
3.3
Sequence Entry
Sequence data files are prepared using a text editor (Notepad,
WordPad, MS Word), and saved in ASCII as text/plain format (.txt)
or in .rtf. The program either takes a single sequence or accepts
multiple separate DNA sequences in FASTA, tabulated format (two
columns from MS Excel sheet or MS Word table), EMBL, MEGA,
GenBank, MSF, DIALIGN, simple alignment, or BLAST Queue
web alignment formats. The template length is not limited. The
FastPCR clipboard allows the user to copy and paste text or tables
from MS Word documents or MS Excel worksheets or other programs
and to paste them into another Office document. It is important that
all target sequences are prepared in the same format. Users can type
or import from file(s) into “General Sequence(s)” or “Additional
sequence(s) or pre-designed primers (probes) list” editors.
FastPCR allows files to be opened in several ways: the original
file can be opened as read-only for editing with text editors; files
can be opened to memory without using text editors, which allows
larger file(s), up to 200 Mb, to be analyzed; files within a folder can
be selected and the files opened during task execution without the
use of text editor program. Additionally, the program can open
files within a selected folder in order to join all these files in a text
editor. For example, this feature can be applied to convert all files
from a selected folder into a single file of FASTA sequences.
Alternatively this feature allows splitting FASTA sequences to indi-
vidual files in a particular selected folder.
When a sequence file is opened, FastPCR displays the informa-
tion about the opened sequence and its format. The information
status bar shows the number of sequences, the total sequence
length (in nucleotides), the nucleotide composition, and the
purine, pyrimidine, CG percentage, and the melting temperature.
Files can be saved in various formats including .rtf, .xls, or txt from
the text editor in use.
FastPCR normally expects to read sequence files in FASTA format
[
10
]. FASTA format has the highest priority and is simple, because
the raw sequence is merely preceded by a definition line. The
definition line begins with a “>” sign and optionally followed
3.4 FASTA Format
Description
