cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly.
cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly.
复制标题
DOI：
10.1093/bioinformatics/bty863
复制
发表时间：
2019-05-15
期刊：
影响因子：
--
通讯作者：
Lees JG
中科院分区：
文献类型：
--
作者：
Lewis TE;Sillitoe I;Lees JG
许多生物信息学领域要求我们将域匹配分配到查询蛋白的延伸上。从一组候选匹配开始，我们想要确定匹配之间有有限/没有重叠的最佳子集。输入数据中的不连续域可能会使情况进一步复杂化。现有的工具越来越多地面对非常大的数据集，它们需要大量的cpu时间和内存。我们提出了一种新的工具，使用在开源c++中实现的动态规划算法来快速处理大型数据集（高达100万次/秒）和合理的内存量。它接受多种输入格式，并以纯文本、JSON或图形HTML提供输出。我们描述了一个针对现有算法的基准测试，它表明CRH在大型数据集上提供了非常相似或略有改进的结果，并且大大提高了CPU/内存性能。CRH网站：https://github.com/UCLOrengoGroup/cath-tools；相关文档可从http://cath-tools.readthedocs.io获得。补充数据可在生物信息学网站获得。
Many bioinformatics areas require us to assign domain matches onto stretches of a query protein. Starting with a set of candidate matches, we want to identify the optimal subset that has limited/no overlap between matches. This may be further complicated by discontinuous domains in the input data. Existing tools are increasingly facing very large data-sets for which they require prohibitive amounts of CPU-time and memory. We present cath-resolve-hits (CRH), a new tool that uses a dynamic-programming algorithm implemented in open-source C++ to handle large datasets quickly (up to ∼1 million hits/second) and in reasonable amounts of memory. It accepts multiple input formats and provides its output in plain text, JSON or graphical HTML. We describe a benchmark against an existing algorithm, which shows CRH delivers very similar or slightly improved results and very much improved CPU/memory performance on large datasets. CRH is available at https://github.com/UCLOrengoGroup/cath-tools; documentation is available at http://cath-tools.readthedocs.io. Supplementary data are available at Bioinformatics online.
登录
查看更多内容
影响因子：
14.9
作者：
Velankar S;Dana JM;Jacobsen J;van Ginkel G;Gane PJ;Luo J;Oldfield TJ;O'Donovan C;Martin MJ;Kleywegt GJ
通讯作者：
Kleywegt GJ
影响因子：
14.9
作者：
Dawson NL;Lewis TE;Das S;Lees JG;Lee D;Ashford P;Orengo CA;Sillitoe I
通讯作者：
Sillitoe I
影响因子：
14.9
作者：
Finn RD;Attwood TK;Babbitt PC;Bateman A;Bork P;Bridge AJ;Chang HY;Dosztányi Z;El-Gebali S;Fraser M;Gough J;Haft D;Holliday GL;Huang H;Huang X;Letunic I;Lopez R;Lu S;Marchler-Bauer A;Mi H;Mistry J;Natale DA;Necci M;Nuka G;Orengo CA;Park Y;Pesseat S;Piovesan D;Potter SC;Rawlings ND;Redaschi N;Richardson L;Rivoire C;Sangrador-Vegas A;Sigrist C;Sillitoe I;Smithers B;Squizzato S;Sutton G;Thanki N;Thomas PD;Tosatto SC;Wu CH;Xenarios I;Yeh LS;Young SY;Mitchell AL
通讯作者：
Mitchell AL
影响因子：
14.9
作者：
Lam SD;Dawson NL;Das S;Sillitoe I;Ashford P;Lee D;Lehtinen S;Orengo CA;Lees JG
通讯作者：
Lees JG
影响因子：
14.9
作者：
Markowitz VM;Chen IM;Chu K;Szeto E;Palaniappan K;Grechkin Y;Ratner A;Jacob B;Pati A;Huntemann M;Liolios K;Pagani I;Anderson I;Mavromatis K;Ivanova NN;Kyrpides NC
通讯作者：
Kyrpides NC