How Can I Run Estscan2 (Perl)

Question

[Mohammad Reza Bakhtiarizadeh]

Hi all, I want to run ESTScan2 (to translate EST sequences to protein)that is written by Perl. i downloaded the package but i don't know how can i run it and unfortunately it hasn't any user guide. if you have any experience about it, please help me. tanks a lot in advance

regards

[Michael]

Don't forget to put here output of what you tried by editing your question. format any console output as code, and provide information on your operating system. Note that installing software, espc. involving compiling code is much easier on Linux than on Windows.

[Michael]

And for specific compilation or install errors use the primary email list.

Answer 1

[Michael]

There are several packages, I assume you took the tar.gz compressed package. The documentation is in the compressed archive, extract it: a README file (). You need to have installed perl and a c-compiler as a precondition to build this, doing this on windows will be more complicated than on linux, if on windows you probably need cygwin for the compilation. Extract the archive like so:

tar xvzf estscan-[?].tar.gz

The README says:

This is a Perl module. It requires my BTLib module, which should be located in the parent directory of this one. They can be built and installed like any other Perl modules:

  cd <BTLib directory>
  perl Makefile.PL
  make install

Actually the BTLib directory is the one you just extracted. To install it globally you might add sudo. Then run ESTscan, it is a perl program. Good luck

[Mohammad Reza Bakhtiarizadeh]

thanks for your help. I downloaded the package from http://sourceforge.net/projects/estscan/ I am freshman about bioinformatics, if possible help me as simple as possible. thanks again for your help. regards

[Michael]

Note, I haven't run that program, but have installed more than enough perl packages. It is always the same.

Answer 2

[Woa]

The latest version ESTScan 3.0 is entirely written in C that bypasses some perl module problems, download and compile that.You can download it from HERE

[Woa]

ESTScan 3.x runs on Linux/Unix and requires a Fortran compiler, the default is G77, I however was able to compile it with GFortran

[Woa]

ESTScan 3.x runs on Linux/Unix and requires a Fortran as well as a C compiler, the default for fortran is G77(see the Makefile) , I however was able to compile it with GFortran

Answer 3

[Federico Giorgi]

It is actually easier to have EstScan3 to run. As pointed out by WoA, EstScan3 is written in C, but the output is identical.

There are eight steps to follow

1. Go to http://sourceforge.net/projects/estscan/files/
2. get the tar.gz of estscan version 3 (estscan)
3. get the tar.gz BTlib latest version (BTLib)
4. get your *smat file from the closest organism (matrices)
5. (optional) if you want to generate you own *smat, follow the manual (documentation)
6. Untar/gunzip everything

7. Install the BTlib perl libraries (thanks Michael)

   cd BTLib
   perl Makefile.PL
   make
   sudo make install
   

8. Compile Estscan

   cd Estscan
   gcc -o estscan estscan.c
   chmod 750 estscan
   

Now you should have a fully functional estscan. You just need to input the matrix file and the fastas.

Like:

./estscan -M matrix.smat yoursequences.fasta

Good luck!

[zqdong2012]

could you help me to fix this problem

estscan: Could not open file /usr/molbio/share/ESTScan/Hs.smat: No such file or directory(2)