Errorneous MITEFinderII output about mitefinder

[nwpuzhengyan]

Thank you for your advise, could you please provide me the input data of you? I want to find the problem by the data

[dipsaha]

Please find below attached a part of the input file as desired by you. Please also let me know about the description of the header line in the output and how to annotate (i) TIR; (ii) TSD; and (iii) MITE classification from the output file. Let me know if you can access the attached file.

sample.fasta.tar.gz

Thanks

[nwpuzhengyan]

Thank you for your advise. I had modified the program and you can run it again. The description of the header line is just like this.

mite|28|586|595|816|825|t3|591|m1|ave_score:0.611172
The 28 means the serial number of chromosome and 586,595,816,825 is the position of TIR. t3 means the length of TSD is 3. The program does not contain the classification of mite, so we run cluster analysis in output file by blastn. If you have any other questions, please contact me by [email protected]. Thank you again.

[dipsaha]

Thanks, the program now worked. But again, I would be glad if scripts are made/posted to extract the TIR and TSD sequences in a batch or at least find them in the header of the output MITE sequences and classify the MITEs based on homology.

Regards
Dip