"... In PAGE 7: ... No cross-hybridisa- tion was observed neither within the set of actin probes nor with the other oligonucleotides included in the chip. These results demonstrated that the oligonucleotide Cross platform comparison To further evaluate the performance of Actichip, we com- pared the microarray with two other well-established oli- gonucleotide-based platforms ( Table4 ). We used 25-mer oligonucleotide commercial chips (Affymetrix, human genome U133A 2.... In PAGE 10: ...e found that 7.0 % or 10.1 % of the Actichip targets were not represented in the Affymetrix GeneChip or Operon array, respectively [see Additional file 2]. This result is not surprising considering that the three array platforms were implemented using different databases or different releases of the same database ( Table4 ) harbouring modi- fications of transcript sequences, identifiers or annota- tions. However, our data question the reliability of the high throughput design of pangenomic probe libraries.... ..."

"... In PAGE 6: ... Although some methods and tools exist for designing probes for microarrays, few online systems have been developed and few can allow users to select sequences dynamically across different virus genera and virus families. Table1 compares the tools and methods for designing oligonucleotide probes. One hundred sequences were randomly selected and the experimental melting temperature of 75oC to 78oC was used to confirm that the LIS_Identity of a probe with its non-target sequence is directly proportional to similarity between the probe and its non-target sequence.... ..."

"... In PAGE 7: ...icroarray. Of these, 32.5% were wild type, 50.6% were heterozygous, and 12% were homozygous for the poly- morphism ( Table1 ). For NAT2*A803G, 80 of 83 (96.... In PAGE 7: ...ig. 1. Representative genotyping results for the NAT2*T341C poly- morphism. Table1 . Genotyping results for NAT2 polymorphisms in this study.... In PAGE 11: ...and negative serum samples were tested simultaneously in three commercial allergen-specific IgE assays, and correlation coefficients were calculated based on all 44 samples ( Table1 ). All of the comparisons produced correlation coefficients .... In PAGE 11: ...1 for cat dander, F13 for peanut, W1 for short ragweed, and D2 for dust mite (D. farinae). Negative samples are identified with an N after the hyphen. In positive samples, the number after the hyphen indicates the ASM score. Table1 . Correlationa between microarray assay and commercial clinical allergen-specific IgE assays.... In PAGE 15: ... These openings, called arrays, enable access to the aluminum oxide substrate. A set of 21mer oligonucleo- tides (Isogen) was synthesized ( Table1 ) and spotted in 325-pL droplets, containing 0.1 mmol/L of the oligonu- cleotide mixture, on the arrays with a Packard BioChip Arrayer (Meriden).... ..."

"... In PAGE 2: ... Gene selection was performed using the GenBank database (release 134,[11]), and was based on a combination of biological knowledge, literature data, Gene Ontology (GO) terms [12] and keywords in the NCBI database. Searches were restricted to genes encoding proteins of the major func- tional groups regulating the dynamics and organisation of the actin cytoskeleton ( Table1 ). Actinome was built fol- lowing a robust protocole as described in the quot;Method quot; section.... In PAGE 3: ... The Actichip probe set was designed to target each of the 327 genes defined in the Actinome database probes designed for 26 genes were shown to target more than one sequence in at least one reference database. We therefore selected either 2 oligonucleotides for 22 genes, 3 for 3 genes or 5 for one gene resulting in a total set of 359 oligonucleotides ( Table1 ). In addition, we used part of a set of viral and bacterial probes described as having no similarity with human transcripts [28] and sequences of human genes reported as being housekeeping genes [29] to generate 41 negative and 32 positive controls, respec- tively.... ..."

"... In PAGE 3: ... Lineage- and phage type-specific and lineage and phage type-dominant ORFs A total of 132 of the 1,751 VAP ORFs were either specific or dominant to a lineage, LSPA type or PT (Table 4, Figure 3). i) S-loop#14/OI#7 Three lineage I and lineage I/II-specific ORFs, ECs0237, ECs0238, and ECs0239, were identified in S-loop#14/ OI#7 by CGH ( Table4 ). The nucleotide sequence [Gen- Bank:EF112439] of this region in the lineage II strain FRIK 920 was homologous to Sakai sequence, except that a Table 1: Summary of BLASTN results of MWG oligonucleotide probes queried against genomes of E.... In PAGE 4: ... coli Sakai. CGH revealed that this region was not only highly divergent but also showed lin- eage- and LSPA type -dominant patterns of divergence ( Table4 ). Among the 31 E.... In PAGE 5: ... coli O157:H7 strains tested. However, 12 ORFs within S-loop#72 were lineage I and lineage I/II-specific ( Table4 ). The nucleotide sequence [GenBank:EF112440] of the FRIK 920 amplifi- cation product obtained for this region had high similar- ity to the E.... In PAGE 7: ....7.1.2); b1200 100% 100% 0% S-loop#85/OI#71 ECs1815 (Z6020) NleF 100% 100% 0% S-loop#85/OI#71 ECs1814 (Z6021) NleH1-2 homolog of Shigella OspG 100% 100% 0% Sp10 ECs1929 (Z2415) putative integrase; b1345 100% 0% 0% Sp10 ECs1930 (Z2414)3 hypothetical protein; ydaQ 100% 0% 8% Sp10 ECs1931 (Z2413)3 hypothetical protein; ydaC 100% 0% 8% Sp10 ECs1932 (Z2412) restriction alleviation and modification enhancement; lar 100% 0% 0% Sp10 ECs1937 (Z2404) phage superinfection exclusion protein; sieB 100% 0% 0% Sp10 ECs19384 hypothetical protein 87% 0% 0% Sp10 ECs1939 (Z2403) hypothetical protein, ydfA 100% 0% 0% S-loop#91 (in Sp10) ECs1941 (Z2400) putative transcriptional regulator 100% 0% 0% S-loop#91 (in Sp10) ECs1942 (Z2399) regulatory protein 100% 0% 0% S-loop#92 (in Sp10) ECs1944 (Z2397) hypothetical protein 100% 0% 0% S-loop#92 (in Sp10) ECs1947 (Z2395) hypothetical protein 100% 0% 0% S-loop#93 (in Sp10) ECs1950 (Z2392) hypothetical protein 100% 0% 0% S-loop#93 (in Sp10) ECs1951 (Z2391) hypothetical protein 100% 0% 0% S-loop#93 (in Sp10) ECs1952 (Z2390) hypothetical protein 100% 0% 0% S-loop#93 (in Sp10) ECs1953 (Z2389) putative methyltransferase 100% 0% 0% S-loop#93 (in Sp10) ECs1954 (Z2387) hypothetical protein 100% 0% 0% S-loop#93 (in Sp10) ECs1955 (Z2386) hypothetical protein 100% 0% 0% S-loop#153 ECs29893 putative regulatory protein 93% 0% 0% S-loop#153/OI#93 ECs2990 (Z3358)5 putative prophage repressor CI 93% 0% 0% S-loop#153/OI#93 ECs2991 (Z3359)5 hypothetical protein 93% 0% 0% S-loop#153/OI#93 ECs2992 (Z3360)5 putative membrane protein 93% 0% 0% 5 Table4 : Distribution of VAP ORFs identified in the microarray study (Continued) Page 7 of 16 (page number not for citation purposes) S-loop#153/OI#93 ECs2993 (Z3361) putative regulatory protein 93% 0% 0% S-loop#153 ECs29943 hypothetical protein 93% 0%... In PAGE 8: ... v) S-loop#78/OI#51 S-loop#78/OI#51, which corresponds to prophage Sp7 in Sakai, contained a cluster of 21 ORFs, located between ECs1574 and ECs1600 of E. coli Sakai, that was absent from all lineage II and lineage I/II strains but present in all lineage I strains ( Table4 ). The S-loop#78 divergent ORFs encoded hypothetical proteins of unknown function and putative bacteriophage-associated proteins.... In PAGE 8: ... Repeated attempts to amplify the divergent region in S-loop#78 by long template PCR with FRIK 920 DNA were unsuccessful. vi) S-loop#83/OI#55 A cluster of 15 lineage I and lineage I/II-specific ORFs, ECs1691-ECs1705, were detected across S-loop#83/ OI#55 and its surrounding sequences ( Table4 ). Five ORFs within the boundaries of S-loop#83, ORFs ECs1693- ECs1697, are homologous to the prrA-modD-yc73-fepC gene cluster located on the pyelonephritis and cystitis pathogenicity island of uropathogenic E.... In PAGE 8: ...biomedcentral.com/1471-2164/8/121 S-loop#153/OI#93 ECs2995 (Z3362)5 putative superinfection exclusion protein 93% 0% 0% S-loop#286/OI#172 ECs5242 (Z5878) putative integrase 80% 100% 0% S-loop#286/OI#172 ECs5245 (Z5881) orf; Unknown function 80% 100% 0% S-loop#286/OI#172 ECs5246 (Z5882) hypothetical protein 80% 100% 0% S-loop#286 ECs5247 hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5248 (Z5884) hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5249 (Z5885) putative resolvase 80% 100% 0% S-loop#286/OI#172 ECs5250 (Z5886) hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5251 (Z5887) hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5252 (Z5888) putative transcription regulator 80% 100% 0% OI#172 Z5889 orf; Unknown function 80% 100% 0% KI#71 b1142 orf, hypothetical protein; ymfH 0% 0% 100% KI#71 b1147 orf, hypothetical protein; ymfL 0% 0% 100% KI#71 b1148 orf, hypothetical protein; ymfM 0% 0% 100% KI#71 b1152 orf, hypothetical protein; b1152 0% 0% 100% KI#121 b2360 orf, hypothetical protein; b2360 0% 100% 100% KI#121 b2361 orf, hypothetical protein; b2360 0% 100% 100% KI#121 b2362 orf, hypothetical protein; b2362 0% 0% 100% KI#121 b2363 orf, hypothetical protein; b2363 0% 0% 100% backbone b1201 putative sensor-type regulator; b1201 0% 100% 100% backbone b1202 putative adhesion and penetration protein; b1202 0% 100% 100% backbone ECs2126 (b1519) putative enzyme 100% 100% 0% backbone ECs2127 (b1520) orf, hypothetical protein 100% 100% 0% Table4 : Distribution of VAP ORFs identified in the microarray study (Continued) Page 8 of 16 (page number not for citation purposes)... In PAGE 9: ...ttp://www.biomedcentral.com/1471-2164/8/121 both Pertactin adhesin and autotransporter domains, respectively. vii) S-loop#85/OI#71 Two lineage I- and lineage I/II-specific ORF were detected in S-loop#85/OI#71, which corresponds to Sakai prophage Sp9 ( Table4 ). The recently described non-LEE encoded effectors nleA, nleH1-2 and nleF are encoded by ORFs ECs1812, ECs1814 and ECs1815, respectively, within this S-loop [31-33].... In PAGE 9: ... coli Sakai. All lineage I/II and lineage II strains and the lineage I PT14 strain LRH6 were diver- gent in Sakai ORFs ECs2989 to ECs2995 within S- loop#153 ( Table4 ). The ORFs ECs2989 and ECs2993 encode putative regulatory proteins, while the others encode hypothetical proteins of unknown function or prophage-related proteins.... In PAGE 9: ... coli Sakai. Ten ORFs in this region in Sakai and EDL933 were present in all lineage I/II strains and all lineage I strains except those of PT 31 but not lin- eage II strains ( Table4 ). The corresponding region [Gen- Bank:EF112443] in E.... In PAGE 9: ... coli K12 and E. coli O157:H7 lineage I/II and lineage II strains ( Table4 ). ORFs b1201 and b1202 encode a puta- tive sensor-type regulator and a putative adhesion and penetration protein, respectively.... ..."

"... In PAGE 3: ... Lineage- and phage type-specific and lineage and phage type-dominant ORFs A total of 132 of the 1,751 VAP ORFs were either specific or dominant to a lineage, LSPA type or PT (Table 4, Figure 3). i) S-loop#14/OI#7 Three lineage I and lineage I/II-specific ORFs, ECs0237, ECs0238, and ECs0239, were identified in S-loop#14/ OI#7 by CGH ( Table4 ). The nucleotide sequence [Gen- Bank:EF112439] of this region in the lineage II strain FRIK 920 was homologous to Sakai sequence, except that a Table 1: Summary of BLASTN results of MWG oligonucleotide probes queried against genomes of E.... In PAGE 4: ... coli Sakai. CGH revealed that this region was not only highly divergent but also showed lin- eage- and LSPA type -dominant patterns of divergence ( Table4 ). Among the 31 E.... In PAGE 5: ... coli O157:H7 strains tested. However, 12 ORFs within S-loop#72 were lineage I and lineage I/II-specific ( Table4 ). The nucleotide sequence [GenBank:EF112440] of the FRIK 920 amplifi- cation product obtained for this region had high similar- ity to the E.... In PAGE 6: ...biomedcentral.com/1471-2164/8/121 Table4 : Distribution of VAP ORFs identified in the microarray study Location ORF Function Lineage I-LSPA 111111 PT2-LSPA 211111 Lineage II-LSPA 222222 n = 15 n = 4 n = 12 S-loop#14/OI#7 ECs0237 (Z0268) RhsG core protein with extension 100% 100% 0% S-loop#14/OI#7 ECs0238 (Z0269) hypothetical protein 100% 100% 0% S-loop#14 ECs0239 hypothetical protein 100% 100% 0% S-loop#16 ECs0272 putative transcription antitermination protein 100% 100% 0% S-loop#16/OI#8 ECs0273 (Z0308) hypothetical protein 100% 100% 0% S-loop#16/OI#8 ECs0274 (Z0309) repressor protein CI 100% 100% 0% S-loop#16 ECs0275 Cro repressor 100% 100% 0% S-loop#16/OI#8 ECs0276 (Z0310) regulatory protein cII 100% 100% 0% S-loop#16/OI#8 ECs0277 (Z0311) replication protein 100% 100% 0% S-loop#16/OI#8 ECs0279 (Z0313) replication protein 100% 100% 0% S-loop#16/OI#8 ECs0280 (Z0317) putative tail fiber protein 100% 100% 0% S-loop#69/OI#45 ECs1160 (Z1424)1 putative integrase 93% 0% 0% S-loop#69/OI#45 ECs1161 (Z1425)1 putative excisionase 93% 0% 0% S-loop#69/OI#45 ECs1162 (Z1426)1 hypothetical protein 93% 0% 0% S-loop#69/OI#45 ECs1163 (Z1428)1 hypothetical protein 93% 0% 0% S-loop#69/OI#45 ECs1219 (Z1475)2 putative small subunit terminase 93% 100% 8% S-loop#69/OI#45 ECs1220 (Z1476)2 putative terminase large subunit 93% 100% 8% S-loop#69/OI#45 ECs1221 (Z1477)2 putative portal protein 93% 100% 8% S-loop#69/OI#45 ECs1222 (Z1478)2 hypothetical protein 93% 100% 8% S-loop#69/OI#45 ECs1223 (Z1479)2 hypothetical protein 93% 100% 8% S-loop#69/OI#45 ECs1224 (Z1480)2 hypothetical protein 93% 100% 8% S-loop#69/OI#45 ECs1225 (Z1481)2 hypothetical protein 93% 100% 8% S-loop#69 ECs1226 2 hypothetical protein 93% 100% 8% S-loop#69/OI#45 ECs1227 (Z1482)2 hypothetical protein 93% 100% 8% S-loop#69/OI#45 ECs1228 (Z1483)2 putative tail fiber protein 93% 100% 8% S-loop#69/OI#45 ECs1232 (Z1486)2 hypothetical protein 93% 100% 8% S-loop#69/OI#45 ECs1233 (Z1487)2 putative tail tip fiber protein 93% 100% 8% S-loop#69 ECs1234 2 putative outer membrane protein 93% 100% 8% S-loop#69/OI#45 ECs1235 (Z1488)2 hypothetical protein 93% 100% 8% S-loop#69/OI#45 ECs1236 (Z1489)2 putative outer membrane precursor 93% 100% 8% S-loop#69/OI#45 ECs1237 (Z1490)2 hypothetical protein 93% 100% 8% S-loop#69/OI#45 ECs1238 (Z1491)2 hypothetical protein 93% 100% 8% S-loop#69/OI#45 ECs1239 (Z1492)2 hypothetical protein 93% 100% 8% S-loop#69/OI#45 ECs1240 (Z1493)2 hypothetical protein 93% 100% 8% S-loop#69/OI#45 ECs1241 (Z1494)2 hypothetical protein 93% 100% 8% S-loop#69/OI#45 ECs1242 (Z1495)2 hypothetical protein 93% 100% 8% S-loop#72/OI#43,48 ECs1377 (Z1635) hypothetical protein 100% 100% 0% S-loop#72/OI#43,48 ECs1378 (Z1636) hypothetical protein 100% 100% 0% S-loop#72/OI#43,48 ECs1379 (Z1637) hypothetical protein 100% 100% 0% S-loop#72/OI#43,48 ECs1382 (Z1640) HecB-like protein 100% 100% 0% S-loop#72/OI#43,48 ECs1383 (Z1641) hypothetical protein 100% 100% 0% S-loop#72/OI#43,48 ECs1384 (Z1642) hypothetical protein 100% 100% 0% S-loop#72/OI#43,48 ECs1385 hypothetical protein 100% 100% 0% S-loop#72/OI#43,48 ECs1386 (Z1643) hypothetical protein 100% 100% 0% S-loop#72/OI#43,48 ECs1387 (Z1644) hypothetical protein 100% 100% 0% S-loop#72/OI#43,48 ECs1388 putative transcriptional regulator, pchD 100% 100% 0% S-loop#72/OI#43,48 ECs1389 (Z1645) hypothetical protein 100% 100% 0% S-loop#72/OI#43,48 ECs1390 (Z1646) hypothetical protein 100% 100% 0% S-loop#78/OI#51 ECs1574 (Z1836) putative integrase 100% 0% 0% S-loop#78 ECs1576 (Z1839) hypothetical protein 100% 0% 0% S-loop#78/OI#51 ECs1578 (Z1840) hypothetical protein 100% 0% 0% S-loop#78 ECs1579 hypothetical protein 100% 0% 0% S-loop#78/OI#51 ECs1580 (Z1841) hypothetical protein 100% 0% 0% S-loop#78 ECs1581 hypothetical protein 100% 0% 0% S-loop#78/OI#51 ECs1582 (Z1842) hypothetical protein 100% 0% 0% Page 6 of 16 (page number not for citation purposes) S-loop#78 ECs1583 hypothetical protein 100% 0% 0% S-loop#78/OI#51 ECs1584 (Z1843) hypothetical protein 100% 0%... In PAGE 8: ... v) S-loop#78/OI#51 S-loop#78/OI#51, which corresponds to prophage Sp7 in Sakai, contained a cluster of 21 ORFs, located between ECs1574 and ECs1600 of E. coli Sakai, that was absent from all lineage II and lineage I/II strains but present in all lineage I strains ( Table4 ). The S-loop#78 divergent ORFs encoded hypothetical proteins of unknown function and putative bacteriophage-associated proteins.... In PAGE 8: ... Repeated attempts to amplify the divergent region in S-loop#78 by long template PCR with FRIK 920 DNA were unsuccessful. vi) S-loop#83/OI#55 A cluster of 15 lineage I and lineage I/II-specific ORFs, ECs1691-ECs1705, were detected across S-loop#83/ OI#55 and its surrounding sequences ( Table4 ). Five ORFs within the boundaries of S-loop#83, ORFs ECs1693- ECs1697, are homologous to the prrA-modD-yc73-fepC gene cluster located on the pyelonephritis and cystitis pathogenicity island of uropathogenic E.... In PAGE 8: ...biomedcentral.com/1471-2164/8/121 S-loop#153/OI#93 ECs2995 (Z3362)5 putative superinfection exclusion protein 93% 0% 0% S-loop#286/OI#172 ECs5242 (Z5878) putative integrase 80% 100% 0% S-loop#286/OI#172 ECs5245 (Z5881) orf; Unknown function 80% 100% 0% S-loop#286/OI#172 ECs5246 (Z5882) hypothetical protein 80% 100% 0% S-loop#286 ECs5247 hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5248 (Z5884) hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5249 (Z5885) putative resolvase 80% 100% 0% S-loop#286/OI#172 ECs5250 (Z5886) hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5251 (Z5887) hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5252 (Z5888) putative transcription regulator 80% 100% 0% OI#172 Z5889 orf; Unknown function 80% 100% 0% KI#71 b1142 orf, hypothetical protein; ymfH 0% 0% 100% KI#71 b1147 orf, hypothetical protein; ymfL 0% 0% 100% KI#71 b1148 orf, hypothetical protein; ymfM 0% 0% 100% KI#71 b1152 orf, hypothetical protein; b1152 0% 0% 100% KI#121 b2360 orf, hypothetical protein; b2360 0% 100% 100% KI#121 b2361 orf, hypothetical protein; b2360 0% 100% 100% KI#121 b2362 orf, hypothetical protein; b2362 0% 0% 100% KI#121 b2363 orf, hypothetical protein; b2363 0% 0% 100% backbone b1201 putative sensor-type regulator; b1201 0% 100% 100% backbone b1202 putative adhesion and penetration protein; b1202 0% 100% 100% backbone ECs2126 (b1519) putative enzyme 100% 100% 0% backbone ECs2127 (b1520) orf, hypothetical protein 100% 100% 0% Table4 : Distribution of VAP ORFs identified in the microarray study (Continued) Page 8 of 16 (page number not for citation purposes)... In PAGE 9: ...ttp://www.biomedcentral.com/1471-2164/8/121 both Pertactin adhesin and autotransporter domains, respectively. vii) S-loop#85/OI#71 Two lineage I- and lineage I/II-specific ORF were detected in S-loop#85/OI#71, which corresponds to Sakai prophage Sp9 ( Table4 ). The recently described non-LEE encoded effectors nleA, nleH1-2 and nleF are encoded by ORFs ECs1812, ECs1814 and ECs1815, respectively, within this S-loop [31-33].... In PAGE 9: ... coli Sakai. All lineage I/II and lineage II strains and the lineage I PT14 strain LRH6 were diver- gent in Sakai ORFs ECs2989 to ECs2995 within S- loop#153 ( Table4 ). The ORFs ECs2989 and ECs2993 encode putative regulatory proteins, while the others encode hypothetical proteins of unknown function or prophage-related proteins.... In PAGE 9: ... coli Sakai. Ten ORFs in this region in Sakai and EDL933 were present in all lineage I/II strains and all lineage I strains except those of PT 31 but not lin- eage II strains ( Table4 ). The corresponding region [Gen- Bank:EF112443] in E.... In PAGE 9: ... coli K12 and E. coli O157:H7 lineage I/II and lineage II strains ( Table4 ). ORFs b1201 and b1202 encode a puta- tive sensor-type regulator and a putative adhesion and penetration protein, respectively.... ..."

"... In PAGE 7: ...icroarray. Of these, 32.5% were wild type, 50.6% were heterozygous, and 12% were homozygous for the poly- morphism ( Table1 ). For NAT2*A803G, 80 of 83 (96.... In PAGE 7: ...ig. 1. Representative genotyping results for the NAT2*T341C poly- morphism. Table1 . Genotyping results for NAT2 polymorphisms in this study.... In PAGE 11: ...and negative serum samples were tested simultaneously in three commercial allergen-specific IgE assays, and correlation coefficients were calculated based on all 44 samples ( Table1 ). All of the comparisons produced correlation coefficients .... In PAGE 15: ... These openings, called arrays, enable access to the aluminum oxide substrate. A set of 21mer oligonucleo- tides (Isogen) was synthesized ( Table1 ) and spotted in 325-pL droplets, containing 0.1 mmol/L of the oligonu- cleotide mixture, on the arrays with a Packard BioChip Arrayer (Meriden).... In PAGE 15: ...nd 55 min are shown in Fig. 1A. The signal increased from 0 to 31 min. The specificity of the binding was determined by changing the hybridization stringency at Table1 . Sequences of the 21mer oligonucleotides.... ..."

"... In PAGE 13: ... 1153 The detailed positions of known sites and putative regulatory sites in the association Y$ARS1_05 = gt; cgccg in a set of ORFs are shown in Table8 . The first column gives the ORFs of yeast in the set and the second shows the detailed positions of known sites and putative regulatory sites in each ORF.... In PAGE 13: ... For each family in Table 7, we extracted the 600 bps upstream sequences in the genes, and used our approach to dis- cover the associations of known site homologs and over-represented oligonucleotides. Table8 shows ms (matching sequences, i.e.... ..."