HHblits是一种经典的多序列比对方法,它基于HMM-HMM比对算法。具体步骤如下: 1.选择一个已知结构的蛋白质作为探针(seed sequence)。 2.在目标数据库中查找与探针相似度较高的序列作为比对目标。 3.利用探针和比对目标的序列构建HMM模型,并进行HMM-HMM比对,得到一组新的比对序列。 4.利用新的比对序列重复步骤3,直...
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(HMMs): 'HMM-HMM–based lightning-fast iterative sequence search' (HHblits;http://toolkit.genzentrum.lmu.de/hhblits/). Compared to the sequence-search tool PSI-BLAST, HHblits is faster owing to its discretized-profile prefilter, has 50–100% higher sensitivity and generates more accurate ...
hhblits_bfd_uniclust_result = self.hhblits_bfd_uniclust_runner.query( File "/lustre/user/lulab/gaojd/whr/alphafold/alphafold/data/tools/hhblits.py", line 143, in query raise RuntimeError('HHblits failed\nstdout:\n%s\n\nstderr:\n%s\n' % ( ...
安装hh-suite hhblits hh-suite # download git clone https://github.com/soedinglab/hh-suite.git cd hh-suite # git pull git submodule init git submodule update # install mkdir build cd build cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=/usr/opt/...
HHblits是一项新的蛋白质研究软件,快如闪电且高度敏感,有望显著提高蛋白质的功能性分析.这项研究发表在2011年12月25日的Nature Methods杂志上。 基本信息 中文名称 同源检测迭代的HMM-HMM的比较 英文名 HHblits 别称 Homology detection by iterative HMM-HMM comparison ...
01.010009 22603932526400 hhblits.py:142] HHblits stderr end Traceback (most recent call last): File "/app/alphafold/run_alphafold.py", line 310, in <module> app.run(main) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/opt...
RuntimeError: HHblits failed#73 LuGarfieldopened this issueJul 29, 2021· 14 comments When I try and build the docker file (trying my best to use consistent versions of software), I always see warnings in the compilation of hhblits. The warnings vary depending the base version of ubuntu use...