Selecting the Right Similarity‐Scoring Matrix
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
Protein sequence similarity searching programs like BLASTP, SSEARCH, and FASTA use scoring matrices that are designed to identify distant evolutionary relationships (BLOSUM62 for BLAST, BLOSUM50 for SSEARCH and FASTA). Different similarity scoring matrices are most effective at different evolutionary distances. ?Deep? scoring matrices like BLOSUM62 and BLOSUM50 target alignments with 20% to 30% identity, while ?shallow? scoring matrices (e.g., VTML10 to VTML80) target alignments that share 90% to 50% identity, reflecting much less evolutionary change. While ?deep? matrices provide very sensitive similarity searches, they also require longer sequence alignments and can sometimes produce alignment overextension into nonhomologous regions. Shallower scoring matrices are more effective when searching for short protein domains, or when the goal is to limit the scope of the search to sequences that are likely to be orthologous between recently diverged organisms. Likewise, in DNA searches, the match and mismatch parameters set evolutionary look?back times and domain boundaries. In this unit, we will discuss the theoretical foundations that drive practical choices of protein and DNA similarity scoring matrices and gap penalties. Deep scoring matrices (BLOSUM62 and BLOSUM50) should be used for sensitive searches with full?length protein sequences, but short domains or restricted evolutionary look?back require shallower scoring matrices. Curr. Protoc. Bioinform . 43:3.5.1?3.5.9. © 2013 by John Wiley & Sons, Inc.
Keywords: similarity scoring matrices; PAM matrices; BLOSUM matrices; sequence alignment
Table of Contents
- Similarity Searching, Homology, and Statistical Significance
- Amino Acid Substitution Matrices: History and Classification
- The Algebra of Similarity Scoring (Log‐Odds) Matrices
- Scoring Matrices and Gap Penalties
- Long Alignments and Overextension
- Scoring Matrices for DNA
- Summary
- Literature Cited
- Figures
- Tables
Materials
Figures
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Figure 3.5.1 The BLOSUM62 matrix. The BLOSUM62 matrix used by BLASTP, BLASTX, and TBLASTN is actually 23 × 23: 20 amino acids plus X (any amino acid), B (D or E), and Z (N or Q). Only the lower half of the symmetric matrix is shown to highlight the identity scores on the diagonal. 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. Weighted by amino acid abundance, the average similarity score is about −1 half‐bits. View Image -
Figure 3.5.2 Comparison of a “shallow” (VTML 20) and “deep” (BLOSUM62) scoring matrix. Both matrices are scaled in 1/2‐bits. For the small part of the matrices shown here, the VTML20 matrix produces an average 2.80 half‐bit identity score, and an average −0.59 nonidentical score (weighted by amino‐acid abundance). In contrast, BLOSUM62 produces 1.86 for identities but only −0.06 for nonidentities. Thus, VTML20 targets shorter, higher‐identity alignments, because it penalizes nonidentities much more strongly. View Image -
Figure 3.5.3 Overextension of an alignment of homologous SH2 domains. (A ) BLASTP alignment of VAV_HUMAN with SKAP2_XENTR. The two proteins share a homologous SH2 domain (highlighted in red) over about 58 amino acids that contributes more than 85% of the similarity score. The remaining 140 amino acid alignment juxtaposes an SH3 domain from VAV_HUMAN (brown) with a Pleckstrin domain from SKAP2_XENTR (green). These two domains are not homologous; they are classified as having different folds in SCOP. (B ) Sub‐alignment scores produced by the SSEARCH36 program using the same scoring matrix as BLASTP (BLOSUM62, 11/1) for the VAV_HUMAN/SKAP2_XENTR alignment. Boundaries for annotated domains in the two proteins were taken from InterPro using the query VAV_HUMAN (qRegion) or the subject SKAP2_XENTR (sRegion). Thus, 103‐206 for the Pleckstrin domain comes from InterPro annotations for SKAP2_XENTR, as does 671‐765 for SH3 domain in VAV_HUMAN. The raw score, bit‐score, and percent identity are shown for the subregions. The Q ‐score is −10log( p ‐value) based on the bit score; thus Q = 30 corresponds to a probability (uncorrected for database size) of 0.001. View Image
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Literature Cited
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