Biology – Quantitative Biology – Biomolecules
Scientific paper
2008-01-16
Bioinformatics. 2008 Jul 1;24(13):i15-23.
Biology
Quantitative Biology
Biomolecules
17 pages, 4 figures, 2 tables
Scientific paper
10.1093/bioinformatics/btn171
The flexibility in gap cost enjoyed by Hidden Markov Models (HMMs) is expected to afford them better retrieval accuracy than position-specific scoring matrices (PSSMs). We attempt to quantify the effect of more general gap parameters by separately examining the influence of position- and composition-specific gap scores, as well as by comparing the retrieval accuracy of the PSSMs constructed using an iterative procedure to that of the HMMs provided by Pfam and SUPERFAMILY, curated ensembles of multiple alignments. We found that position-specific gap penalties have an advantage over uniform gap costs. We did not explore optimizing distinct uniform gap costs for each query. For Pfam, PSSMs iteratively constructed from seeds based on HMM consensus sequences perform equivalently to HMMs that were adjusted to have constant gap transition probabilities, albeit with much greater variance. We observed no effect of composition-specific gap costs on retrieval performance.
Altschul Stephen F.
Gertz Michael E.
Stojmirović Aleksandar
Yu Yi-Kuo
No associations
LandOfFree
The effectiveness of position- and composition-specific gap costs for protein similarity searches does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with The effectiveness of position- and composition-specific gap costs for protein similarity searches, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and The effectiveness of position- and composition-specific gap costs for protein similarity searches will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-392374