No description, website, or topics provided.
R Perl
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Failed to load latest commit information.


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  ./ ../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.

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).