How to determine the boundary or the region of ITS1 (internal transcribed space 1) , specially for ciliates

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Rumakanta Sapkota

You can use ITSx,very useful tool for ITS extraction in the link. For detail visit the link http://microbiology.se/software/itsx/

Shahed Uddin Ahmed Shazib

Thanks for your suggestion,, i m windows user,, but this software is only for Linux / MacOsX. Do u have any alternative idea ?

Because many bioinformatics software are in Linux, try to download Visual Box or Cygwin terminal in your windows PC. This will provide Linux environment in your PC

If it is too complicated for you, simply download few related sequences long enough to cover ITS1 and 5.8s from NCBI and align your desired sequences with these sequences. Since 5.8s is highly conserved, you can locate the boundary