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Support for BCL::Jufo Software
Technical support is available throughout the license period.
For scientific or technical questions related to BCL::Jufo, please contact us.
If there is a major bug fix or significant improvements to the application, entities with current licenses will be notified via email and will be given access to the updated software.
Installation Procedures
BCL::Jufo
Copy the appropriate BCL::Jufo executable into the respective directory on your PC. You will need to select the executable appropriate for the site-licensed PC operating system:
bcl_jufo_x86.exe [Linux 32-bit executable]
bcl_jufo_x86_64.exe [Linux 64-bit executable]
bcl_jufo_win32.exe [Windows 32-bit executable]
No additional steps are required for installation. If there are major bug fixes or revisions, an email will be sent out to entities with current licenses so that the newest application can be installed.
PsiBlast
In order to run BCL::Jufo, PsiBlast must be installed. Free downloads can be found at http://www.ncbi.nlm.nih.gov/BLAST/download.shtml. Please make sure to download the version for the correct platform and follow all instructions on the screen.
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. For more information please visit http://blast.ncbi.nlm.nih.gov/.
Running BCL::Jufo
GETTING INSTRUCTIONS OR HELP AT THE COMMAND LINE Helpful information concerning syntax and flags can be obtained by typing the following (simply substitute the file name of your executable):
For more general information about the product, type
HOW TO RUN THE APPLICATION
Running BCL::Jufo consists of three main steps.
1.) Create the fasta sequence file for the protein to be studied. You will need the protein sequence in fasta format for both BCL::Jufo and PsiBlast, and it should be stored in a <.fasta> file. An example is given below. For more information about fasta formats, please visit http://www.ncbi.nlm.nih.gov/blast/fasta.shtml.
2.) Create the PsiBlast position-specific scoring matrix. Run PsiBlast on the fasta sequence to produce a PsiBlast position-specific scoring matrix with extension .ascii. More information on running PsiBlast and adjusting various parameters can be found in the documentation which accompanied the download.
An example run of PsiBlast at the command line could look like the following, where $MyDataBase and $MyBlastProfile are the names of the database used and desired PsiBlast position-specific scoring matrix output file respectively:
3.) Run BCL::Jufo. At a command prompt, navigate to the location of your BCL::Jufo executable program. The syntax for running the application looks like the following:
BCL::Jufo needs a fasta sequence with the extension .fasta and a PsiBlast position-specific scoring matrix file with the extension .ascii to exist in the same directory.
FLAG
-pdbid <prefix>
The application finds fasta and Blast needed to run BCL::Jufo by adding .fasta and .ascii extensions to the <prefix> value provided. The <prefix> value is usually a four letter pdb code such as 1UBI but also can include path /home/user/sequences/1UBI.
-output <output_filename>
By default the output file is created with name <prefix> + .Jufo. The user can specify a different output name by providing it at <output_filename> such as sequence.Jufo or /home/user/sequences/1UBI.Jufo.
INPUT AND OUTPUT.
BCL::Jufo requires two inputs, a fasta file and a corresponding PsiBlast position-specific scoring matrix. The fasta file uses one letter codes for protein sequence and looks like the following:
The PsiBlast position-specific scoring matrix on the other hand looks like following: Last position-specific scoring matrix computed, weighted observed percentages rounded down, information per position, and relative weight of gapless real matches to pseudocounts
A R N D C Q E G H I L K M F P S T W Y V A R N D C Q E G H I L K M F P S T W Y V
1 M -4 -4 -5 -6 -4 -4 -5 -6 -5 4 2 -4 9 -3 -5 -4 -3 -4 -4 -1 0 0 0 0 0 0 0 0 0 24 13 0 63 0 0 0 0 0 0 0 1.72 1.27
2 Q -4 3 1 -1 -6 5 1 -5 -1 -2 -3 3 -1 -2 -4 -1 -2 2 -2 -5 0 15 6 3 0 32 6 0 1 3 2 20 1 1 0 4 2 3 1 0 0.74 1.36
Column 1: Amino acid position
Column 2: One letter code for amino acid type
Column 3: One letter code for the predicted secondary structure; U=Undefined/Loop, S=Strand, H=Helix
Column 4: Undefined/Loop probability (between 0 and 1) for this amino acid
Column 5: Helix probability (between 0 and 1) for this amino acid
Column 6: Strand probability (between 0 and 1) for this amino acid
