Using blastn to look for intron/exons boundries

[alexa039]

Hi All
I am try to align RNAseq data to a genome to map the exons using blastn. The sequence alignment output terminates at the exact end of the alignment. I would like to see some additional bases at the end of the subject sequence so as to see where the GT/AG sequence is in the genomic sequence. I cant seem to see an option in the blastn manual. I saw some options such as best_hit_overhang but it didn't give the desired output.

Thanks in advance

[Jose Blanca]

For doing just that, we first do a blast to locate the region and then a est2genome alignment.
You can take a look at the Python code that we use. The function is named infer_introns_for_cdna and is in github:

https://github.com/JoseBlanca/franklin/blob/master/franklin/seq/seq_analysis.py

[alexa039]

Thanks very much Jose.