IMPALA: Integrating Matrix Profiles And Local Alignments

1. Files in Distribution

The following IMPALA source code files are distributed:

copymat.c 
impatool.c
makemat.c  
posit2.c
profiles.c       
newkar.c
profiles.h
Makefile

2. Compilation

Run the following commands in the directory, containing IMPALA source code files:

make makemat
make copymat
make impala

This will result in three binary executable files:

makemat : primary profile preprocessor 
  (converts a collection of binary profiles, created by the -C option
   of PSI-BLAST, into portable ASCII form);

copymat : secondary profile preprocessor 
  (converts ASCII matrices, produced by the primary preprocessor, 
   into database that can be read into memory quickly);

impala          : search program (searches a database of score 
  matrices, prepared by copymat, producing BLAST-like output).

3. Conversion of profiles into searchable database

3.1. Primary preprocessing

Prepare the following files:

i.      a collection of PSI-BLAST-generated profiles with arbitrary 
       names and suffix .chk; 

ii.     a collection of "profile master sequences", associated with 
    the profiles, each in a separate file with arbitrary name and a 3 character
    suffix starting with c;
    the sequences can have deflines; they need not be sequences in nr or
    in any other sequence database; if the sequences have deflines, then
    the deflines must be unique.

iii.    a list of profile file names, one per line, named 
    <database_name>.pn;

iv.     a list of master sequence file names, one per line, in the same 
    order as a list of profile names, named 
     <database_name>.sn;

The following files will be created:

i.      a collection of ASCII files, corresponding to each of the 
      original profiles, named 
     <profile_name>.mtx;

ii.     a list of ASCII matrix files, named 
      <database_name>.mn;

iii.    ASCII file with auxiliary information, named 
       <database_name>.aux;

Arguments to makemat:

    -P database name (required)
    -G Cost to open a gap (optional)
       default = 11
    -E Cost to extend a gap (optional)
       default = 1
    -U Underlying amino acid scoring matrix (optional)
       default = BLOSUM62
    -d Underlying sequence database used to create profiles (optional)
       default = nr
    -z Effective size of sequence database given by -d
       default = current size of -d option
       Note: It may make sense to use -z without -d when the
       profiles were created with an older, smaller version of an
       existing database 
    -S  Scaling factor for  matrix outputs to avoid round-off problems
       default = PRO_DEFAULT_SCALING_UP (currently defined as 100)
       Use 1.0 to have no scaling
       Output scores will be scaled back down to a unit scale to make
       them look more like BLAST scores, but we found working with a larger
       scale to help with roundoff problems.
    -H get help (overrides all other arguments)
Note: It is not enforced that the values of -G and -E passed to makemat
were actually used in making the checkpoints. However, the values fed
in to makemat are propagated to copymat and impala.

3.1. Secondary preprocessing

Prepare the following files:

i.      a collection of ASCII files, corresponding to each of the 
  original profiles, named 
  <profile_name>.mtx 
(created by makemat);

ii.     a collection of "profile master sequences", associated with 
  the profiles, each in a separate file with arbitrary name and a 3 character
  suffix starting with c.

iii.    a list of ASCII_matrix files, named 
     <database_name>.mn 
   (created by makemat);

iv.     a list of master sequence file names, one per
  line, in the same order as a list of matrix names, named 
  <database_name>.sn;

v.      ASCII file with auxiliary information, named 
  <database_name>.aux 
(created by makemat);

The files input to copymatices are in ASCII format and thus portable 
between machines with different encodings for machine-readable files

The following files will be created:

i.      a huge binary file, containing all profile matrices, named
 <database_name>.mat;

Arguments to copymat

    -P database name (required)
    -H get help (overrides all other arguments)

4. Search

Before you start searching, check that you have copies of or soft
links to all the files associated with the PSSM library. If the
library has K PSSMs, you should have

     K files with names ending in .mtx
     K files with names ending in a 3-letter extension starting with c
     1 file with name ending in .pn
     1 file with name ending in .sn
     1 file with name ending in .aux
     1 file with name ending in .mn
     1 file with name ending in .mat

Arguments to impala

   -i  query sequence file (required)
   -P  database of profiles (required)
   -o  output file (optional)
       default = stdout
   -e  Expectation value threshold  (E), (optional, same as for BLAST)
       default = 10 
   -m  alignment view (optional, same as for BLAST)
   -z  effective length of database (optional)
       -1 = length given via -z option to makemat
       default (0) implies  length is actual length of profile library
          adjusted for end effects
   -H  get help (overrides all other options)

5. Directory convention

  Since IMPALA requires a large number of files, it may be convenient
to store your impala files in various directories. For copymat,
makemat, and impala the following parsing convention applies
to the string that follows the -P argument.
If the string starts with a '/', then it is deemed to be a full
path name. Whatever prefix occurs upto and including the rightmost
'/' is deemed to be a prefix that should be prepended to all
file names in the .sn, .pn, and .mn files.

Example: If you call any of the 3 programs including the
   argument -P /foo/bar/wolf1187
then
   /foo/bar/ is prepended to every filename listed in 
       wolf1187.pn
       wolf1187.sn
       wolf1187.mn
   before opening the file, but the files
       wolf1187.pn
       wolf1187.sn
       wolf1187.mn
   themselves are not changed.

6. Output

IMPALA output closely mimics output of BLASTP family programs and
should be compatible with SEALS BLAST parsers.

Send suggestions, comments, complaints only to Alejandro Schaffer
schaffer@helix.nih.gov


Reference:

  Schaffer, A.A., Wolf, Y.I., Ponting, C.P. Koonin, E.V.,
Aravind, L., Altschul, S. F., IMPALA: Matching a Protein Sequence 
Against a Collection of PSI-BLAST-Constructed Position-Specific 
Score Matrices, Bioninformatics, to appear.

Please cite the above paper if you publish any results computed by IMPALA.