Abstract not found

Genomic sequence databases are widely used by molecular biologists for homology searching. Amino-acid and nucleotide databases are increasing in size exponentially, and mean sequence lengths are also increasing. In searching such databases, it is desirable to use heuristics to perform computationally intensive local alignments on selected sequences only and to reduce the costs of the alignments that are attempted. We present an index-based approach for both selecting sequences that display broad similarity to a query and for fast local alignment. We show experimentally that the indexed approach results in signi cant savings in computationally intensive local alignments, and that index-based searching is as accurate as existing exhaustive search schemes.

Intrinsic protec disorde reord toseDO: ts or towhole prote%k that fail to foldcomplejDE onthej own. HeE we preO:kEb disorde onproteO seteO[E from 34gek:]O[ including 22 bacteDk[ 7 archae% and 5eD:%# ote% Pre%#8Eb disorde8] sesor ts # 50, # 40, and # 30 in leEO% we% deD#:Eb8[ as weD asprote#k eote#kE to be whollydisordeD]: The five eEkO] otewe] seD#Eb8# frombacte#D and archae by havingthe highe: pe8j[ tage ofsekDkkkE preDkkkE to have disorde8j sesor ts # 50 inleDk]: from 25% for Plasmodium to 41% for Drosophila. Estimate of whollydisorde:% protede inthe bactej[ range from 1% to 8%, avek8Oj% to 32%, e%,EO%D8 in various archae range from 2 to 11%, plus anappare tly anomalous 18%, avek[%%O to 75% that drops to 53% ifthe high value isdiscarde8 Estimate inthe 5ekD%[ arange from 3 to 17%.The putative whollydisorde:k protede we8 ofte ribosomalproteEk: but in addition abouteE%% numbe% we% of known and unknown function. OveE8jk intrinsic disorde app to be a common, withethE% ote peDDO# having ahighe pe888 tage of native disorde than archae or bacte#Eb Keywords: intrinsicdisorde% prede%O]: structuralgeructu 1

this paper. In any case, the general idea of comparing genomes in terms of protein structures is expected to be a very fertile topic in the future. There are currently seven microbial genomes completed and at least 36 more being worked on (Kerlavage, 1997), so there will be many possibilities for comparison soon

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