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Arabidopsis
c_elegans
s_cerevisiae
README

README

how to blastp:

makeblastdb -in worm_mart_export.fa -dbtype prot -parse_seqids -hash_index -out worm_mart_export 
   87  blastp -query uniprot-ec%3A-+AND+reviewed%3Ayes.fasta -db worm_mart_export -out ../Results/alluniprot.blasted -outfmt 7 -evalue 5e-2 -num_threads 5
  107  ./1_filter_blast_results_dictionary.pl ../Data/uniprot_EC_dictionary.txt ../Results/blasted_query_gene.txt 



Requires perl module LWP::Simple for downloading enzime infromation from KEGG database
Require a working BLAST+ installation and the path of the directory containing the blast executable programs must be added to the PATH environment variable. 
Also a formatbd formated database of a fasta file of all protein sequences of the organism of interest is needed and similarity matrix of the genes of interest computed using expression data.

Usage:
Run the scripts in the provided order (as described in the paper), first the scripts in the Metabolic_network directory and later the scripts in the Blast_Gold_standard directory (see README uder each directory for detailed information).