T-tracking program ?

Victor Jongeneel vjongene at isrec-sun1.unil.ch
Tue Dec 22 07:58:22 EST 1992


Jarmo Niemi TUY (JANIEMI at FINABO.ABO.FI) wrote:

: I am looking for a program, that helps one to identify the
: position of a clone in a sequence by running only one
: sequencing reaction (so-called T-tracking). Some sources,
: like Deininger's review (Anal. Biochem 135(1983)247-263) and
: Amersham's sequencing leaflet state that this can be done
: by computer, but I haven't so far found any reference to
: a program that would do it. 

Jarmo,

A T-track identification method has been published by Golovanov and
Nedospasov in CABIOS 2:297, 1986.  It has the great advantage of _not_
making you guess the gap between groups of T's, which would be the
greatest source of errors if you used "classical" sequence analysis
programs such as those found in GCG.  The principle is that it
generates a numerical code for a T-track which is based on the
occurrences of T singlets and multiplets in a nucleotide
sequence.  The code obtained from a gel can then be compared to a
"library" of codes generated from the reference sequence.

I do not have the program source code available, but can direct you to
Sergei Nedospasov if you want it.  My guess is that it would be a
trivial programming job anyway, once the technique is understood.

Good luck!


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C. Victor JONGENEEL                       vjongene at isrecmail.unil.ch
Ludwig Institute for Cancer Research
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