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hhblits output

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uniprot20

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hhblits: lightning-fast iterative protein sequence searching by hmm-hmm alignment

HHblits is a protein sequence search tool that works by iterative pairwise comparison of profile hidden Markov models. We implemented both filters with streaming SIMD extension 3 (SSE3) instructions, which are available on all modern Intel and Advanced Micro Devices (AMD) central processing units and process 16
4 Jan 2012 The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). It contains HHsearch [1] and HHblits. [2] among other programs and utilities. HHsearch takes as input a multiple sequence alignment. (MSA) or
3 Nov 2007 You can also run the query HMM against other databases. • Try to use manualPSI-BLAST iterations (use FASTA in first round if you can) to try to find more distant homologs for your query alignment and jump-start HHsearch with the manually enriched alignment. • Try out other structure prediction servers!:
wget https://github.com/soedinglab/hh-suite/ … ce.tar.gz. \end{verbatim}. \vspace{2mm}. \item Then unzip and untar the file.
bioinformatics hh-suite hhblits alignment sequence-search profile-search profile-profile-search opensource cpp hhsearch hhpred protein-structure. The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden
DESCRIPTION. HHblits version 2.0.16 (January 2013): HMM-HMM-based lightning-fast iterative sequence search HHblits is a sensitive, general-purpose, iterative sequence search tool that represents both query and database sequences by HMMs. You can search HHblits databases starting with a single query sequence,
configure --prefix=/home/you/. During the ./configure step, an information is printed about which dependencies could not be found and have to be configured manually after the installation. Here is an example: OK: Java found. OK: Rscript found. OK: randomForest library found. FAILED: HHblits not found, remember to adjust
The HH-suite is an open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases. Sequence searches are a standard tool in modern biology with which the function of unknown proteins can be inferred from the
Please consult the ModPipe Manual for detailed information about these hits modes. Since the hits mode handling has changed in the development version of ModPipe, the manual of the latest release doesn't cover the changes especially the newest options (HHBlits and HHSearch). A public release is planned for early
29 Jul 2011 the average time needed for the entire HHblits search. Sequences that pass the first two steps are aligned in a third step using SSE2 instructions to determine the region likely to contain the true alignments. For back-tracing the alignments, we need to prevent the score from saturating. Therefore, each score
     

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