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Old 01-14-2011, 09:12 AM   #1
alexa039
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Default Using blastn to look for intron/exons boundries

Hi All
I am try to align RNAseq data to a genome to map the exons using blastn. The sequece 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
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Old 01-14-2011, 11:32 AM   #2
rdu
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I dont have an answer. Instead, I suggest you to switch your question to "Bioinformatics" section, because I can get replies soon after my questions being posted there. Good luck!
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Old 01-14-2011, 11:45 AM   #3
alexa039
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thanks for the advice
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