"Sister-scanning" is a
method for measuring variations in the relatedness of aligned nucleotide
sequences along their length. These variations result from recombination, from
differential selection or from random changes. The significance of detected
variations is tested in the program using Monte Carlo randomization procedures.
This enables misleading signals resulting from, for example, similarities of
composition, to be discounted. In this,Version 2.0, 'synonymous',
'non-synonymous' and all differences between sequences can be examined
separately. The SiScan program produces an output file in MS-Excel format, so
that the signals, and Z scores based on them, may be displayed graphically.
Version 1.04 is the latest update of
the original package. It has many associated programs and it is capable of
producing tree diagrams as postscript files. It also produces data files in
different formats so that other applications such as PHYLIP,WINAMOVA, DIPLOMO,
etc can be used. In response to many requests Version 2.00 has been developed
to enable much larger datasets to be examined. However it does not have all the
functions of the original version as programs for drawing trees are limited to
about 200 samples. These programs which come from other programmers are memory
limited; one, for example, uses a recursive routine which requires large
amounts of storage. The README files in th epackages give more details of the
differences. We have fully functional packages of Version 1.04 with other
limits, which we will send when requested.
Version 1.04 Limits: 100 Samples, 20
Populations, 250 Bands,20 Primers
Version 2.00 Limits: 250 Samples, 50
Populations, 3000 Bands,50 Primers
This package contains programs to
help with the design of PCR primers for a group of aligned related nucleotide
sequences; it is also useful for searching sequences for taxonomically
informative differences. It is written in Fortran and operates under DOS
in the Command Line via a simple Batch file menu, and the outputs require a
line editor and Excel. The aligned sequences are examined using a sliding
window technique to find regions of minimal variability. The programs
calculate properties of potential primer sites, namely their Tm, self- and
cross-hybridization potential, and there is also a program for searching a file
of sequences with a redundant sequence. The sequences must be provided in a
single file in NBRF/PIR or FASTA format. This version will handle up to 100 sequences,
each of 25,000 nucleotides.
