map_align

map_align takes two contact maps and returns an alignment that attempts to maximize the number of overlapping contacts while minimizing the number of gaps.

Update

• (20Feb2018) A new implementation that works directly with PDB structures: https://github.com/gjoni/map_align

Installation

$ g++ -O3 -std=c++0x -o map_align main.cpp

For parallel version:

$ g++ -O3 -std=c++0x -o map_align_omp main_omp.cpp -fopenmp

Usage

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MAP_ALIGN
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-a             contact map A               [REQUIRED]
-b             contact map B               [REQUIRED]
-gap_o         gap opening penalty         [Default=-1]
-gap_e         gap extension penalty       [Default=-0.01]
-sep_cut       seq seperation cutoff       [Default=3]
-iter          number of iterations        [Default=20]
-silent
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Advanced options
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-range_a       trim map A to specified range(s) (eg. 0-20 50-100)
-range_b       trim map B to specified range(s)
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Experimental features
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-use_gap_ss    penalize gaps at secondary structure elements(SSE)
-gap_ss_w      gap penality weight at SSE  [Default=2]
-use_prf       use sequence profile
-prf_w         profile weight              [Default=1]
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$ map_align -a A.map -b B.map

contact map format

• LEN 440 - [len]gth
• CON 0 4 1.0 - [con]tact, i, j and weight.
• PRF 0 A H 0.01 ... 0.01 (optional) profile, i, amino acid (AA), secondary structure (SS) and profile frequencies (20 values). The order of the frequencies does not matter, as long as they match between the two contact maps being compared. H = Helix; E = Sheet; all other characters treated equally.

parsing output

• the output will be a single line (if -silent is used).
  • MAX params map_a map_b contact_sco gap_sco total_sco aln_len 0:0 1:1 2:2 ...
  • the alignment is provided as 0:0 with index of first and second map.
  • if "-use_prf" flag is used, the output will include an extra profile_sco column:
    • MAX params map_a map_b contact_sco gap_sco profile_sco total_sco aln_len 0:0 1:1 2:2 ...

Experimental features

• WARNING: these are experimental features and may not work correctly!
• "gap_ss" uses the SS info provided in the "PRF" line to increasing gap penalities within secondary structure elements, favoring gaps in loop or regions of missing density.
• "prf" uses the frequencies provided in the "PRF" line to assist in alignment. This option was intented to help align regions void of contact information. The average frequencies of input profiles (from both maps) is used to compute the background frequencies. WARNING: This option may hurt finding the optimial alignment when aligning non-homologous proteins that share the same fold due to convergent evolution.

Convert GREMLIN/CCMPRED results to .map files

• See mk_map directory!

Convert PDB to .map files

• See mk_map directory!