[EMBOSS] needle question!
kehayden at gmail.com
Thu Feb 8 17:17:52 EST 2007
I am currently using needle to generate an alignment between two
sequences which contain non-informative bases (ie, identified low
quality bases (phred scores) and have been changed to "N").
Presently, these bases are penalized as any other non-matching
character. Is there any way to change needle to "overlook" these
bases when generating the best scoring alignment (or, do I need to
write my own version of needle?)
Thank you in advance for any advise you can offer!
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