We could detect easily 5.8S as a region of ITS through online (http://rfam.sanger.ac.uk/) but not ITS1 and ITS2 regions of macrofungi DNA sequences. Does anybody have any idea how to detect ITS1 and ITS2 regions in a fungi DNA sequence?
Try this excellent and very useful software by Henrik Nilsson: FungalITSextractor. http://www.emerencia.org/FungalITSextractor.html
@ Guillaume Nicolas: Thanks for the link. I noticed it before but file formate (FungalITSExtractor.pl) is not working in my notebook (Thinkpad-lenovo). Do you know this formate will work in windows7? Many thanks again.
as advice, you should partition your notebook with a linux operating system (such as UBUNTU, UNIX) like that you can use many useful bioinformatics software more easily. I dont know if fungalextractor works on windows7.
Depending on the organisms you are working with you could even find the very conserved 3'end of the 18S and the 5'end of the 25/28S rDNA by eye. Also the 5.8S rDNA is easy to find - comparing various organisms.
you can always install a virtual machine and use that to run your OS specific software to make it compatable.
https://www.virtualbox.org/
Try the new ITS (http://microbiology.se/software/itsx/)
Article at
https://www.researchgate.net/publication/252931467_Improved_software_detection_and_extraction_of_ITS1_and_ITS2_from_ribosomal_ITS_sequences_of_fungi_and_other_eukaryotes_for_analysis_of_environmental_sequencing_data?ev=prf_pub
Article Improved software detection and extraction of ITS1 and ITS2 ...
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