000114843 001__ 114843
000114843 005__ 20181203021031.0
000114843 037__ $$aARTICLE
000114843 245__ $$aImproving the sensitivity of the sequence profile method
000114843 269__ $$a1994
000114843 260__ $$c1994
000114843 336__ $$aJournal Articles
000114843 500__ $$aSwiss Institute for Experimental Cancer Research (ISREC), Epalinges.
000114843 520__ $$aThe sequence profile method (Gribskov M, McLachlan AD, Eisenberg D, 1987, Proc Natl Acad Sci USA 84:4355-4358) is a powerful tool to detect distant relationships between amino acid sequences. A profile is a table of position-specific scores and gap penalties, providing a generalized description of a protein motif, which can be used for sequence alignments and database searches instead of an individual sequence. A sequence profile is derived from a multiple sequence alignment. We have found 2 ways to improve the sensitivity of sequence profiles: (1) Sequence weights: Usage of individual weights for each sequence avoids bias toward closely related sequences. These weights are automatically assigned based on the distance of the sequences using a published procedure (Sibbald PR, Argos P, 1990, J Mol Biol 216:813-818). (2) Amino acid substitution table: In addition to the alignment, the construction of a profile also needs an amino acid substitution table. We have found that in some cases a new table, the BLOSUM45 table (Henikoff S, Henikoff JG, 1992, Proc Natl Acad Sci USA 89:10915-10919), is more sensitive than the original Dayhoff table or the modified Dayhoff table used in the current implementation. Profiles derived by the improved method are more sensitive and selective in a number of cases where previous methods have failed to completely separate true members from false positives.
000114843 700__ $$aLuthy, R.
000114843 700__ $$aXenarios, I.
000114843 700__ $$0244404$$aBucher, P.$$g113607
000114843 773__ $$j3$$k1$$q139-46$$tProtein Sci
000114843 909C0 $$0252244$$pGR-BUCHER$$xU11780
000114843 909CO $$ooai:infoscience.tind.io:114843$$pSV$$particle
000114843 937__ $$aGR-BUCHER-ARTICLE-1994-002
000114843 973__ $$aOTHER$$rREVIEWED$$sPUBLISHED
000114843 980__ $$aARTICLE