Update README.md

Machine-Learning-for-Structural-Bioinformatics/README.md

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+#!/bin/bash
+
+# This script is used to download and extract uniprot20, uniref90 and nr
+
+################################ 1. Download and extract uniprot20_2016_02 (Takes approximately 35 minutes to download, 15 minutes for installation) ############################
+cd ./lib/hhsuite
+wget -r -np -k  -nd http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/uniprot20_2016_02.tgz
+tar -xvzf uniprot20_2016_02.tgz
+rm uniprot20_2016_02.tgz
+echo "Done with downloading and extracting uniprot20_2016_02!"
+cd ../../
+
+
+
+####################### 2. Download and extract uniref90 (Takes approximately 7-8 minutes to download, and 45 minutes to several hours for installation) ##########################
+mkdir ./lib/uniref90
+cd ./lib/uniref90
+wget -r -np -k  -nd ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz
+gunzip uniref90.fasta.gz
+cp ../../lib/blast/bin/formatdb ./
+./formatdb -i uniref90.fasta
+rm uniref90.fasta.gz
+echo "Done with downloading and extracting uniref90!"
+cd ../../
+
+
+
+################################# 3. Download nr and extract nr (It takes approximately 4 minutes to download and 5-10 minutes for installation) ################################
+
+cd ./lib
+wget -r -np -nd ftp://zhanglab.ccmb.med.umich.edu/download/nr.tar.gz
+tar -xvzf nr.tar.gz
+rm nr.tar.gz
+echo "Done with downloading and extracting nr!"
+cd ../