MTRAP is a sequence alignment program by a new measure based on transition probability between two consecutive pairs of residues.

Build & Install

$ cmake .
$ make
$ sudo make install

Trouble shoots:

• if make failed, try ./clean.sh to clean up unnecessary files.

Usage

mtrap [OPTIONS] inputfile outputfile

===   OPTIONS  ===
= GENERAL =
-I                  [...]  add search path e.g. -I ~/mymatrix
-filelist           [...]
-i                  [...]  input file (FASTA format)
-o                  [...]  output file
-nosort                    the results are not sorted
-noestimation                 do not estimate a family
-cds      [GENETICCODES (comma separate)]  "protein" coding DNA sequence
             GENETICCODE 0: The Standard Code (transl_table=1)
                         1: The Vertebrate Mitochondrial Code (transl_table=2)
                         2: The Invertebrate Mitochondrial Code (transl_table=5)
                         3: The Bacterial, Archaeal and Plant Plastid Code (transl_table=11)

= GAP =
-go                 [-11]  gap open [score]
-ge                [-0.3]  gap extension [score]

= MULTIPLE ALIGNMENT =
-itr                 [10]  set the number of iterations
-c                    [2]  set the number of consistency transformations

= SUBSTITUTION MATRIX =
-m             [VTML200I]  substitution matrix e.g. CGONNET250, EBLOSUM62
-rm              [MRAMA1]  ramachandran matrix e.g. MRAMA1
-averageExtendedAA                 average extended amino acids (B,Z and X) substitutions

= TRANSITION QUANTITY MATRIX =
-tm       [SABmark1.63_sup_weighted.btq]  transition-quantity matrix
-e                [0.775]  epsilon, weight for transition quantity

= RAMACHANDRAN QUANTITY =
-gamma                [0]  gamma, weight for ramachandran matrix

= PARTITION FUNCTION POSTERIOR PROBABILITY =
-pf                 [0.7]  the degree of partition function
-pm            [VTML200I]  substitution matrix used for partition function
-pgo                [-22]  gap open [score] for partition function
-pge                 [-1]  gap extension [score] for partition function
-beta               [0.2]  beta, weight for partition function
-beta2              [1.5]  beta2, weight for a part of TQ of partition function

= GENERATING MODE =
-primarylibrary           [ID]  output T-Coffee primary library, ID: sequence identity (same as T-Coffee)

-count    [MODES FILELIST WEIGHTLIST]  count the frequency of transition
           MODES 0: normal 1:skip gap-gap site 2:set zero gap site
                 3: direct prob 4: without lower case 5: global TQ
                 f: symmetrize the frequencies not the tq
                 n: do not round the substitution matrix
-outbintm      [FILENAME]  output binary format transition-quantity matrix

Version 2

MTRAP version 2 uses the following state-of-the-art approaches in addition to Transition-quantity.

• Partition function posterior probability
• Iterations & consistency transformations

These are introduced by ProbCons

As a result, profile matrix is calculated as below:

1. Calculate profile := pf * (MTRAP profile) + (1 - pf) * (posterior probability profile), where MTRAP profile is the paper version profile, i.e. e * Transition-quantity + (1 - e) * Score-matrix.

2. Smooth the profile by using iterations & consistency transformations.

Documents

• Making transition quantity
• Details of the dynamic programming
• Resources
• Utility scripts

Links

• Original site: Ohya Lab. (Ohya Lab. was closed)
• Paper: Hara T., Sato K., Ohya M., "MTRAP: Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues", BMC Bioinformatics 2010, 11:235. link

License

MTRAP is released under the terms of the MIT license.

Note that the previous versions (before version 2) was licensed under BSD.

MTRAP uses the following open source libraries

• Eigen 3.1.2 (MPL2 License)
• Snappy 1.0.5 (BSD License)