## What is protein scoring matrix?

Every program for searching protein sequences against a database includes a choice of a protein weight matrix, also called a scoring matrix. In general, scoring matrices implicitly represent a particular theory of protein sequence evolution.

**Which Blosum scoring matrix should you use for closely related proteins?**

BLOSUM matrices with high numbers are designed for comparing closely related sequences, while those with low numbers are designed for comparing distant related sequences. For example, BLOSUM80 is used for closely related alignments, and BLOSUM45 is used for more distantly related alignments.

### What is PAM and Blosum?

The PAM matrices are based on scoring all amino acid positions in related sequences, whereas the BLOSUM matrices are based on substitutions and conserved positions in blocks, which represent the most-alike common regions in related sequences. The choice of which matrix to use depends on the goals of the investigator.

**What do we use position specific scoring matrices for?**

In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences. Searching with PSSMs in complete genomes or large sequence databases is a common, but computationally expensive task.

## How does a position weight matrix work?

Position weight matrix (PWM) is a scoring matrix composed of the log likelihood of each nucleotide in a motif (TFBS). With multiple sequence alignment, the PWM is derived from the most frequent TFBSs of a specific TF. Traditionally, PWMs are used in hit-based methods to predict TF-binding.

**How do you find the score of a matrix?**

Scoring matrices are used to determine the relative score made by matching two characters in a sequence alignment. These are usually log-odds of the likelihood of two characters being derived from a common ancestral character.

### How do you choose a BLOSUM matrix?

In general a few rules apply to the selection of scoring matrices.

- For closely related sequences choose BLOSUM matrices created for highly similar alignments, like BLOSUM80.
- For distant related sequences, select low BLOSUM matrices (for example BLOSUM45) or high PAM matrices such as PAM250.

**What BLOSUM matrix would be ideal for identifying similar homologs?**

The BLOSUM62 matrix The most positive value is 11 ( ‘W:W’ alignment); the most negative is −4 (found for many hydrophobic/hydrophilic and small/large replacements). The BLOSUM62 matrix is scaled in 1/2-bit units, so the W:W alignment of 11 is 25.5=45 times more common in homologous proteins than by chance.

## What does a high BLOSUM score mean?

The interpretation is that the higher the score, the more likely the corresponding amino-acid substitution is. The wikipedia article on BLOSUM has a good explanation, check the section on scoring.

**What is an amino acid substitution scoring matrix?**

An amino acid substitution scoring matrix encapsulates the rates at which various amino acid residues in proteins are substituted by other amino acid residues, over time. Database search methods make use of substitution scoring matrices to identify sequences with homologous relationships.

### Are there any disordered regions in proteins used in substitution scoring matrices?

However, widely used substitution scoring matrices, such as BLOSUM series, have been developed using aligned blocks that are mostly devoid of disordered regions in proteins.

**What are the standard scoring matrices?**

The group of matrices referred to as Standard includes BLOSUM, PAM, MD 32 and VTML 33, 34 series of scoring matrices which are routinely used as default matrices in the popular homology search tools such as SSEARCH/FASTA 35 and BLAST 36.

## What happens if the matrix average or expected score is positive?

If the matrix average or expected score is positive, alignments will extend to the ends of the sequences, and become global, rather than local 43.