Absolutely! The probability of introducing a gap at a given position is much smaller (~10 times) than the probability that the gap will include more than just a single amino acid. Gaps do not grow by linear addition of amino acids. The problem is that we do not have good physico-chemical models how indels are generated, just empirical observations. These seem to indicate that an exponential extension term would be better than a linear one, but it is computationally more costly. There is literature on that, which you should be able to find ... for example Gaston Gonnet's 1992 study (newer studies would probably cite that one so you can find them through the citation index): Gonnet GH, Cohen MA, Benner SA. Exhaustive matching of the entire protein sequence database. Science. 1992 Jun 5;256(5062):1443-5. HTH Boris On 14 Jul 2006, at 09:58, Theodore H. Smith wrote: > > Do bio-informaticians normally expect a Needleman-Wunsch > implementation, to allow for differing gap open and gap extension > penalties? > > Or is it normal to just have a linear gap penalty. > _______________________________________________ > Biodevelopers mailing list > Biodevelopers at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biodevelopers