Position-specific scoring matrix

The effect of PSI-BLAST is to attune the scoring scheme to the query, and in practice this may or may not be desirable. On one hand, PSI-BLAST can be very sensitive to remote homology on the other hand, spurious sequences may be included and their scores may become inflated. Previously we used NP 000764 as a BLAST query to identify CYP2E1 homologs now we use NP 000764 to initiate a PSI-BLAST search. The first round of PSI-BLAST yields the same BLAST results 

To demonstrate the improved sensitivity of the PSl-BLAST approach, the sequence of histidine triad (HIT) protein was used as a database search query. Simi- 

---

Proteins Using Position-Specific Scoring Matrices. 248... 

IMPALA matching a protein sequence against a collection of PSI-BLAST-constructed position-specific scoring matrices. Bioinformatics, in press. 

Jones, D. T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202. 

Gowri VS, Krishnadev O, Swamy CS et al (2006) MulPSSM a database of multiple position-specific scoring matrices of protein domain families. Nucleic Acids Res 34 D243-D246... 

Henikoff, J. G. and S. Henikoff, Using substitution probabilities to improve position-specific scoring matrices. ComputAppl Biosci, 1996. 12(2) p. 135-43. 

Panchenko, A. R. and Bryant, S. H. (2002) A comparison of position-specific score matrices based on sequence and structure alignments. Protein Sci. 11, 361-370. 

Frith, M. C., Spouge, J. L., Hansen, U., and Weng, Z. (2002) Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res. 30, 3214-3224. 

Jones, D.T. Protein secondary structure prediction based on position-specific scoring matrices. 

Position-specific Scoring Matrices. Available http //bioinf.cs.ucl.ac.uk/psipred/. 

---