The effectiveness of position- and composition-specific gap costs for protein similarity searches.
The effectiveness of position- and composition-specific gap costs for protein similarity searches.
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DOI：
10.1093/bioinformatics/btn171
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发表时间：
2008-07-01
期刊：
影响因子：
--
通讯作者：
Yu YK
中科院分区：
文献类型：
--
作者：
Stojmirović A;Gertz EM;Altschul SF;Yu YK
动机：间隙成本的灵活性所享有的隐马尔可夫模型（HHHRM），预计将提供更好的检索精度比位置特定的评分矩阵（PSSMs）。我们试图量化的影响，更一般的差距参数分别检查的位置和组合物的具体差距分数的影响，以及通过比较的检索精度的PSSM构建使用迭代程序的阻碍提供的Pfam和SUPERFAMILY，策划合奏的多重比对。结果：我们发现，位置特异性缺口罚分比统一缺口成本具有优势。我们没有探索优化每个查询的不同均匀间隙成本。对于Pfam，从基于HMM共有序列的种子迭代构建的PSSM与调整为具有恒定间隙转移概率的Hacks表现相当，尽管具有大得多的方差。我们没有观察到组合特定的差距成本检索性能的影响。这些结果表明PSI-BLAST蛋白质数据库搜索程序可能有所改进。可用性：可根据作者的要求提供执行评估的脚本。Contact:yyu@ncbi.nlm.nih.gov
Motivation: 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. Results: 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. These results suggest possible improvements to the PSI-BLAST protein database search program. Availability: The scripts for performing evaluations are available upon request from the authors. Contact:yyu@ncbi.nlm.nih.gov
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DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
DOI：
10.1016/s0097-8485(96)80004-0
发表时间：
1996-03-01
期刊：
COMPUTERS & CHEMISTRY
影响因子：
--
作者：
Gribskov, M;Robinson, NL
通讯作者：
Robinson, NL
Pfam：氏族、网络工具和服务。
影响因子：
14.9
作者：
Finn, Robert D.;Mistry, Jaina;Schuster-Bockler, Benjamin;Griffiths-Jones, Sam;Hollich, Volker;Lassmann, Timo;Moxon, Simon;Marshall, Mhairi;Khanna, Ajay;Durbin, Richard;Eddy, Sean R.;Sonnhammer, Erik L. L.;Bateman, Alex
通讯作者：
Bateman, Alex
影响因子：
5.6
作者：
KROGH, A;BROWN, M;HAUSSLER, D
通讯作者：
HAUSSLER, D
影响因子：
5.8
作者：
Price, GA;Crooks, GE;Brenner, SE
通讯作者：
Brenner, SE