Hey there,
I am not sure where to put that so I opened a thread here.
I have a bunch of short nucleotide sequences (21 nts). My goal is to align these sequences to all introns of the TAIR10 genome of Arabidopsis. Additionally, in each of the sequences one nucleotide was exchanged.
My first thought was to create a position specific matrix (to include the positional effects of the mutated nucleotides) and then run the alignment againts the TAIR10 sequences.
Does anyone know any appropriate software to do this? And perhaps you have a better solution to do this.
I am not sure where to put that so I opened a thread here.
I have a bunch of short nucleotide sequences (21 nts). My goal is to align these sequences to all introns of the TAIR10 genome of Arabidopsis. Additionally, in each of the sequences one nucleotide was exchanged.
My first thought was to create a position specific matrix (to include the positional effects of the mutated nucleotides) and then run the alignment againts the TAIR10 sequences.
Does anyone know any appropriate software to do this? And perhaps you have a better solution to do this.
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