ReBLOSUM :: Rectangular BLOSUM Matrices

What is ReBLOSUM

The Rectangular BLOSUM matrices give scores to compare amino acid groups from different alphabets. In some indexing applications, memory constraints require some grouping of amino acids. The ReBLOSUM matrices can be used when only one alphabet is compressed : for example, a 4x20 matrix is far more precise than a square 4x4 matrix.

Alphabets names are those defined in [Edgar 04] and gather the works of [Li 03] and other papers. The reference BLOSUM implementation is the one from [Henikoff 92]. Parameters "lambda" and "K" for the e-value are computed according to [Karlin 90].

You can get all the matrices using the Li alphabets on an unique web page, or in an unique zip file.

Get a specific matrix

Alphabet 1
20 - standard alphabet on amino acids
16 - C FY W ML IV G P A T S N H QE D R K
8 - CFYW MLIV G P ATS NH QED RK
custom :
other predefined :
Alphabet 2
20 - standard alphabet on amino acids
16 - C FY W ML IV G P A T S N H QE D R K
8 - CFYW MLIV G P ATS NH QED RK
custom :
other predefined :

BLOSUM Threshold :

References

Rectangular BLOSUM matrices are a collaboration between Symbiose team (IRISA, CNRS, INRIA, Univ. Rennes 1) and Bonsai team (LIFL, CNRS, INRIA, Univ. Lille 1). Please cite :

Principal references used in ReBLOSUM (see the article for a full list) :