psl alignment format and qstarts- qends calculation
Entering edit mode
7.7 years ago
vasilislenis ▴ 150

Hello everybody,

I'm trying to make a method in order to generate an proximate alignment among two whole mammalian genomes in quick time. At the moment in order to evaluate my results I want to convert my output into psl format.

My problem is that I cannot understand the way of the calculation of the qstarts and tstarts values (the two last values) for the negative strand. At the positive strand, the qstarts will be the same with starting position at the query and the tstarts will be the starting position of the target.

For the negative strand, if you will see the following example:

132     22      0       0       0       0       0       0       -       chr24   61756751        49146459        49146613        chr22   61598339        1042089 1042243 1       154, 12610138,       1042089,

how are being calculated the last two numbers?

Thank you very much in advance,


pairwise-alignment psl whole-genome • 1.7k views
Entering edit mode

I would suggest you to retrieve the output in blast format in order to understand what is represented in psl format.


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