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Clustal X 1.8 is a windows interface for the Clustal W
multiple sequence alignment program. It provides an integrated environment for
performing multiple sequence and profile alignments and analyzing the results.
The sequence alignment is displayed in a window on the screen. A versatile
coloring scheme has been incorporated allowing to highlight conserved features
in the alignment. The pull-down menus at the top of the window allows to select
all the options required for traditional multiple sequence and profile
alignment.
PRIMER is a computer program for selecting PCR
primer pairs to amplify specific regions of sequenced DNA. While PRIMER was
specifically designed to select primers from cloned and sequenced genomic DNAs,
many of the tests it performs are useful for selecting oligos for other types
of experiments as well, including other PCR applications, oligo hybridization
and dideoxy sequencing.
For any given sequence, PRIMER applies a
variety of analyses which determine: (1) Which "target" subsequence
should be amplified. (2) Which of the possible primers flanking the target will
be compatible with specific PCR reaction conditions, such as annealing
temperature. (PRIMER computes annealing
temperature based on recent experimental measurements of base-stacking
energies, rather than simply counting A-T and G-C base pairs). (3) Whether the
primers (or the target sequence itself) have a significant degree of
complimentarity to known repeat elements possibly resulting in nonspecific
annealing and amplification. (4) Whether the primers have a significant degree
of complimentarity to themselves or to each other. (5) Whether the PCR product
itself has the desired size and GC content.
Once configured for specific criteria, PRIMER
can apply these tests to many input sequences in an automated manner. PRIMER also allows user to interactively
test specific primers designed using some other primer designing software or
manually designed primer, against these criteria.
To create all input files and to read primer
0.5 out put files standard software packages (e.g., word processors, Notepad)
were required. To create a sequence (".seq") file by hand the format
was that the first line of information for each sequence is the sequence name
which follows the "*sequence: " identifier. After this, several other lines of information may be given.
Similarly a repeat (".rep") file can be created in the same way,
although an included sample of repeat file is useful. The criteria file
(".cri") was most easily created when PRIMER interactively prompts
through the process. PRIMER assumes
that all data files reside in the same directory (or folder) that was open when
the program was invoked.