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ConSurf

  • Description

    is a bioinformatics tool designed for estimating the evolutionary conservation of amino and nucleic acid positions in protein, DNA, and RNA molecules. It leverages phylogenetic relationships among homologous sequences to assess conservation, providing insights into structural and functional importance. ConSurf employs advanced computational methods, including empirical Bayesian and maximum likelihood approaches, to deliver accurate evolutionary rate estimations.

  • Usage

    To list all executables provided by ConSurf, run: $ biogrids-list consurf Copy to clipboard

  • Usage Notes

    ConSurf requires BLAST-formatted databases in /programs/local/consurf/1.0.0/

    To download the DBs: cd /programs/local/consurf/1.0.0/ curl -kLO ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz curl -kLO ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz gunzip uniprot_sprot.fasta.gz gunzip uniprot_trembl.fasta.gz

    Format with formatdb (not makeblastdb): formatdb -i uniprot_sprot.fasta -p T formatdb -i uniprot_trembl.fasta -p T

    To use databases elsewhere, edit /programs/x86_64-linux/consurf/1.0.0/share/consurf/consurfrc.default and change the paths under [databases].

  • Installation

    Use the following command to install this title with the CLI client: $ biogrids-cli install consurf Copy to clipboard Available operating systems: Linux 64
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