|Syntactic Confectionery Delight|
Re: Re: BioInformatics - polyA tail searchby MiamiGenome (Sexton)
|on Sep 02, 2003 at 18:17 UTC||Need Help??|
I do apologize for the sparse details.
A polyA tail can be defined as a string of length 10 or greater containing only 'A' or 'N'.
The files to search contain 80 character lines terminated with a control-M, as follows :
ACGGAAAATCGGATCTGAATGTCTAGAGGGGTTCTCTCCCTTGGTGTGAGTCTAGCCCTGAAAGTTGCCACTCATTGAGC^M CGTTGCCGACTGAGGCTTTGGACTCCAAGGGTAAGGAGCAGACGATGGAGGACGATTTGCTTTGGGGCATCACGCAACCA^M TCCCACTCTCGCGAAGCCAAATTTGTCGAGAGTACTCTGGGGGGAAGAGATCAGAATTGTGCAGACTAATCCGTAACTGC^M CAAGTACTATTGGCCCTGTTCCAACCATCTAACCTCCTTATGATAACCATGCCACTAAATGGGTTCCTGGATCTGCACCT^M CATTCGCTCGCCTTATGGCCTCGGCTCTCTGCGTATCCACCCTCCTCGTCACCGCCATGCCCTTCGACCTTCAGCGGGGG^M
Thus far, I have used only grep, but I think the control-M may be imbedded in some of the poly A stretches.
Thank you again!