Hello all. I am unsure if this is the correct forum, but was referred here wit sort of a unique question.
I have a run of over 1000 sequences, in ABI format. Each read is relatively short, less than 1 kb. Our goal is to align/analyze each read together - but to do so we must first eliminate sequence from both the 5' and 3' ends.
We typically do this by "hand" in Geneious, using unique restriction sites at both the 5' and 3' ends. Simply put, we delete sequence upstream of one restriction site and then everything downstream of another restriction site (which is also downstream of the first restriction site.)
With less than 100 sequences, this is just a few hours of work. However with over 1000 reads, it gets to be very time consuming!
Does software exist which would allow me to do this sequence editing in a batch format? I believe we're looking for something which would identify two restriction sites in a read, and delete the sequence either upstream or downstream of those sites. Below is the general idea, in case the description above is not clear.
Thanks for any help,
Ray
I have a run of over 1000 sequences, in ABI format. Each read is relatively short, less than 1 kb. Our goal is to align/analyze each read together - but to do so we must first eliminate sequence from both the 5' and 3' ends.
We typically do this by "hand" in Geneious, using unique restriction sites at both the 5' and 3' ends. Simply put, we delete sequence upstream of one restriction site and then everything downstream of another restriction site (which is also downstream of the first restriction site.)
With less than 100 sequences, this is just a few hours of work. However with over 1000 reads, it gets to be very time consuming!
Does software exist which would allow me to do this sequence editing in a batch format? I believe we're looking for something which would identify two restriction sites in a read, and delete the sequence either upstream or downstream of those sites. Below is the general idea, in case the description above is not clear.
Thanks for any help,
Ray
Comment