MMLSUM

Minimum Message Length SUbstitution Matrix (modelling evolutionary amino acid interchanges in protein sequences)

Reference: D. Sumanaweera, L. Allison, & A. S. Konagurthu, "Bridging the Gaps in Statistical Models of Protein Alignment" [PDF (published)] [arXiv (preprint)]

Markov matrix related

Markov matrix (t=1): A stochastic matrix of amino acid conditional probabilities (at 0.01 expected change). Exponentiate this matrix (M^t) to get a stochastic matrix for any time=t.
Time-dependent 3-state machine transition probabilities: Associated time-dependent 3-state machine probabilities

MMLSUM Code and Raw Data

Download

Converted log-odds integer-valued scoring matrices

(Note: Default gap open/extn penalties derived from inferred Dirichlet distributions are printed in the respective file headers)

MMLSUM_Expected_Change_10%: Log-Odds scoring matrix for sequences with expected 10% amino acid change.
MMLSUM_Expected_Change_20%: Log-Odds scoring matrix for sequences with expected 20% amino acid change.
MMLSUM_Expected_Change_30%: Log-Odds scoring matrix for sequences with expected 30% amino acid change.
MMLSUM_Expected_Change_40%: Log-Odds scoring matrix for sequences with expected 40% amino acid change.
MMLSUM_Expected_Change_50%: Log-Odds scoring matrix for sequences with expected 50% amino acid change.
MMLSUM_Expected_Change_60%: Log-Odds scoring matrix for sequences with expected 60% amino acid change.
MMLSUM_Expected_Change_70% ---> (Use this for general-purpose): Log-Odds scoring matrix for sequences with expected 70% amino acid change.
MMLSUM_Expected_Change_80%: Log-Odds scoring matrix for sequences with expected 80% amino acid change.
MMLSUM_Expected_Change_90%: Log-Odds scoring matrix for sequences with expected 90% amino acid change.

Download all MMLSUM log-odds matrices (integer and real valued).

Converted log-odds real-valued scoring matrices

(Note: Default gap open/extn penalties derived from inferred Dirichlet distributions are printed in the respective file headers)

MMLSUM_Expected_Change_10%: Log-Odds scoring matrix for sequences with expected 10% amino acid change.
MMLSUM_Expected_Change_20%: Log-Odds scoring matrix for sequences with expected 20% amino acid change.
MMLSUM_Expected_Change_30%: Log-Odds scoring matrix for sequences with expected 30% amino acid change.
MMLSUM_Expected_Change_40%: Log-Odds scoring matrix for sequences with expected 40% amino acid change.
MMLSUM_Expected_Change_50%: Log-Odds scoring matrix for sequences with expected 50% amino acid change.
MMLSUM_Expected_Change_60%: Log-Odds scoring matrix for sequences with expected 60% amino acid change.
MMLSUM_Expected_Change_70% ---> (Use this for general-purpose): Log-Odds scoring matrix for sequences with expected 70% amino acid change.
MMLSUM_Expected_Change_80%: Log-Odds scoring matrix for sequences with expected 80% amino acid change.
MMLSUM_Expected_Change_90%: Log-Odds scoring matrix for sequences with expected 90% amino acid change.

Download all MMLSUM log-odds matrices (integer and real valued).

Supplementary material associated with the MMLSUM's paper:

Download Supplementary Data (gzipped tarball: ~74MB compressed; 210MB uncompressed)