我正在尝试设置 PSIPRED 以运行二级结构预测,但 README.md 文件不够详细,无法让像我这样的初学者设置和运行 PSIPRED。我正在尝试将它与 BLAST+ 一起使用。
我使用的是 Linux Ubuntu 17.04 操作系统,以下是我尝试设置 PSIPRED 的步骤。似乎缺少我不确定如何安装或找到它们所在位置的程序以及缺少的命令:
sudo apt install ncbi-blast+ #OK: Install BLAST+
wget http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/psipred.4.01.tar.gz #OK: Get the latest PSIPRED
tar xzvf psipred.4.01.tar.gz #OK: Extract the latest PSIPRED
rm psipred.4.01.tar.gz #OK: Remove the the latest PSIPRED .tar.gz download
cd psipred/src #OK: Go to source code directory
make #OK: Compile PSIPRED binaries
make install #OK: Compile PSIPRED binaries
cd .. #OK: Go back to PSIPRED top level directory
wget ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz #OK: Download the latest uniref90 database
gunzip -v uniref90.fasta.gz #OK: Uncompress the latest uniref90 database
bin/pfilt uniref90.fasta > uniref90filt #ERROR HERE: pfilt not found. Cannot find where the pfilt program is and cannot find from where to install it from
formatdb -t uniref90filt -i uniref90filt #ERROR HERE: formatdb not found. Cannot find where the formatdb program is and cannot find from where to install it from
makeblastdb -dbtype prot -in uniref90filt -out uniref90filt #OK: Not sure what this does but it works fine
./BLAST+/runpsipredplus example/example.fasta #ERROR HERE: /usr/local/bin/psiblast: Command not found. FATAL: Error whilst running blastpgp - script terminated!
我怎样才能让 PSIPRED 工作?我做错了什么?我在哪里可以获得使 PSIPRED 工作所需的所有外部程序?我错过了什么?