I am browsing through the Biostring on-line docu,mentation. I wonder whether the illustarted techniques (functions) for Pairwise Sequence Alignments are being usd in any of the packages aimed at predicting miRNA target-genes match. I only haveonly used miRANDA which makes us of the Smith-Waterman algorithm. However I cannot recognize any of Biostring techniques for sequence alignment. I may be confused by the lack of documentation & comments in miRANDA C code. Thank you in advance, Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

On Sun, Aug 9, 2009 at 10:15 AM, <mauede@alice.it> wrote: > I am browsing through the Biostring on-line docu,mentation. I wonder > whether the illustarted techniques (functions) for Pairwise Sequence > Alignments are being usd in any of the packages aimed at predicting miRNA > target-genes match. > I only haveonly used miRANDA which makes us of the Smith-Waterman > algorithm. However I cannot recognize any of Biostring techniques for > sequence alignment. I may be confused by the lack of documentation & > comments in miRANDA C code. > Thank you in advance, > Hi, Maura. This not an answer to your question, but miRNA target prediction is not just a function of pairwise alignment and is a research field unto itself (and not a field I am closely aligned with), so your best bet is to use published algorithms and predictions unless you have a specific need to improve on existing techniques (which implies understanding every detail of what they do). Sean [[alternative HTML version deleted]]