promals with 3D information

This program is free for academic use.

1. Install promals

   Operating system: Linux; Unix; Mac OS X
   System requirements: g++; gcc; g77; python; awk
                
   This whole package is about 8GB. The main disk-consuming part is
   sequence and structure databases. Please check if your computer 
   has enough free disk space before installation.
        
   Installation instructions:  
                
       1.1 Download 'promals_package.tar.gz' to your computer. 
           Extract files using gunzip and tar.

              gunzip promals_package.tar.gz
              tar xf promals_package.tar
                
       1.2 Go to the directory 'promals_package':

              cd promals_package

       1.3 Run the following command:

              python install.py
              (pay attention to error or warning messages)

              This will install promals and other programs promals uses, 
              including:
                  - blastpgp (for running PSI-BLAST)
                  - cd-hit (for initial clustering of sequences)
                  - mafft (for alignment of closely related sequences)
                  - psipred (for secondary structure prediction)
                  - TMalign (for structural alignment)

              You need to install the following programs by yourself.
                - 'DaliLite' (for structural alignment) is not installed by this
              package. To use this program, you need to install it by yourself 
              (due to license of DaliLite), and put the 'DaliLite' executable 
              in the 'bin/' directory inside this package. DaliLite is available
              at: http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads

                - 'fast' (for structural alignment) is not installed by this package.
              To use this program, you need to install it by yourself, and put
              the 'fast' executable in the 'bin/' directory inside this package.
              'fast' is available at: http://biowulf.bu.edu/FAST/download.htm
              Make sure you have 'fast' executable of the correct platform.
        
       1.4 Check if the python script file 'promals' is generated in
           the 'bin/' directory, which should also include executables of
           blastpgp, cd-hit, fast, TMalign, mafft, runpsipred1, makemat, 
           al2co_consensus and promals_c.

2. Run promals

        Use the 'promals' (a python script) in the bin/ direcory.
        
        Command: 

            promals input_file [options] > input_file.log
                    or 
            python promals input_file [options] > input_file.log

            Example: 
               promals yfp.fa > yfp.fa.log
               promals yfp.fa -id_thr 0.6 -blast_dir yfp.fa_blast -outfile yfp.promals.aln > yfp.fa.log
        
        Input: 
                input_file needs to be in fasta format

        Output: 
                Two alignment files will be generated. One is a clustal 
                format alignment (file name can be specified by option -outfile). 
                The other file is an html file of colored alignment.
 
        Options:

        Any option name (starting with '-') and its value are separated by white space.  

        For alignment strategies:
         -id_thr [0, 1]          Identity threshold that determined the partition of
                                 fast and slow alignment processes. If two groups of
                                 sequences has average identity above this threshold,
                                 align them in a fast way. Otherwise, use slower but
                                 more accurate way (by profile-profile alignment with
                                 predicted secondary structures and available 3D 
                                 constraints). Default: 0.6 (corresponding to 60% identity)

        For using 3D information:
         -dali [0 or 1]          Use DaliLite structural alignment (1) or not use 
                                 fast alignment (0) ("DaliLite" executable needs to 
                                 be present in bin/ directory). Default: 0 (it is 
                                 relatively slow to run DaliLite)
         -fast [0 or 1]          Use fast structural alignment (1) or not use fast 
                                 alignment (0) ("fast" executable needs to be present 
                                 in bin/ directory). Default: 1
         -tmalign [0 or 1]       Use TMalign structural alignment (1) or not use fast 
                                 TMalign alignment (0) ("TMalign" executable needs to 
                                 be present in bin/ directory). Default: 1
         -struct_weight [0, inf[ Weight of structural constraints relative to sequence 
                                 constraints. Default: 1.5

        For profile scoring:
         -ss_weight [0,inf[      Weight of predicted secondary structure in profile-
                                 profile scoring. Default: 0.2
         -score_weight [0,inf[   Weight of amino acids in profile-profile scoring. 
                                 Default: 0.8

        For running PSI-BLAST to get sequence profile:
         -iter_number       Number of PSI-BLAST iterations for profile generation. 
                                 Default: 3
         -evalue [0, inf[        PSI-BLAST evalue cutoff for inclusion. Default: 0.001
         -low_id_thr [0,1]       Remove PSI-BLAST hits with identity to the query less 
                                 than this value.  Default: 0.2
         -blast_dir        Directory of running PSI-BLAST and store other 
                                 intermediate results.
         -clean_blast_before [0 or 1]  Remove any file in the directory that stores 
                                 intermediate results (specified by -blast_dir option) 
                                 before running PSI-BLAST. Default: 0. 
         -clean_blast_after [0 or 1] Remove any file in the PSI-BLAST directory after 
                                 running PSI-BLAST. Default: 0

        For output:
         -outfile          The name of output alignment file.
         -blocksize         Number of letters in clustal-format alignment blocks. 
                                 Default: 70
         -resnum [0 or 1]        In colored html alignment, show residue numbers for 
                                 alignment blocks. Default: 1
         -caa_freq [0, 1]        In colored html alignment, show amino acid consensus
                                 symbol if the fraction of a class of residues is higher
                                 than this threshold. Default: 0.8

3. Contact: Jimin Pei (jpei [AT] chop [DOT] swmed [DOT] edu)
   Please report bugs during installation or when running promals.

4. References

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST
and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res
1997, 25:3389-3402.
Holm L, Sander C: Mapping the protein universe. Science 1996, 273:595-603.
Jones DT: Protein secondary structure prediction based on position-specific scoring matrices.
J Mol Biol 1999, 292:195-202.
Katoh K, Kuma K, Toh H, Miyata T: MAFFT version 5: improvement in accuracy of multiple
sequence alignment. Nucleic Acids Res 2005, 33:511-518.
Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein
or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
Pei J, Grishin NV: PROMALS: towards accurate multiple sequence alignments of distantly
related proteins. Bioinformatics 2007, 23:802-808.
Pei J, Kim BH, Grishin NV: PROMALS3D: a tool for multiple protein sequence and structure
alignments. Nucleic Acids Res 2008, 36:2295-2300.
Zhang Y, Skolnick J: TM-align: a protein structure alignment algorithm based on the
TM-score. Nucleic Acids Res 2005, 33:2302-2309.
Zhu J, Weng Z: FAST: a novel protein structure alignment algorithm. Proteins 2005, 58:618-627.