Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties-4

<p><b>Copyright information:</b></p><p>Taken from "Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties"</p><p>http://www.biomedcentral.com/1471-2105/8/356</p><p>BMC Bioinformatics 2007;8():356-356.</p><p>Published online 21 Sep 2007</p><p>PMCID:PMC2048517.</p><p></p>core bin. In figures 1B and C, pairs were also binned by relative size difference (the difference is defined as the relative size of the smallest protein of a query-hit pair compared the largest in %

Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties-3

<p><b>Copyright information:</b></p><p>Taken from "Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties"</p><p>http://www.biomedcentral.com/1471-2105/8/356</p><p>BMC Bioinformatics 2007;8():356-356.</p><p>Published online 21 Sep 2007</p><p>PMCID:PMC2048517.</p><p></p>ins belonging to COG1487 is 84). Proteins starting with MT belong to . The tree was visualised with TreeView [26]

Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties-0

<p><b>Copyright information:</b></p><p>Taken from "Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties"</p><p>http://www.biomedcentral.com/1471-2105/8/356</p><p>BMC Bioinformatics 2007;8():356-356.</p><p>Published online 21 Sep 2007</p><p>PMCID:PMC2048517.</p><p></p>core bin. In figures 1B and C, pairs were also binned by relative size difference (the difference is defined as the relative size of the smallest protein of a query-hit pair compared the largest in %

Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties-1

<p><b>Copyright information:</b></p><p>Taken from "Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties"</p><p>http://www.biomedcentral.com/1471-2105/8/356</p><p>BMC Bioinformatics 2007;8():356-356.</p><p>Published online 21 Sep 2007</p><p>PMCID:PMC2048517.</p><p></p>ibutes 1/(total number of hits of query) to the relevant bin. Figure 2A shows the number of pairs with and without gene order conservation, Figure 2B the number of pairs per size bin

Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties-2

<p><b>Copyright information:</b></p><p>Taken from "Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties"</p><p>http://www.biomedcentral.com/1471-2105/8/356</p><p>BMC Bioinformatics 2007;8():356-356.</p><p>Published online 21 Sep 2007</p><p>PMCID:PMC2048517.</p><p></p>of a specific label as the e-value threshold that gives the same positive predictive value as a BLAST search not using label information (a more detailed description is given in the main text). Figure 3B shows the average number of homologs per query when equivalent e-values are used as thresholds in cases where genes of a query-hit pair share gene order or are of similar size

LocateP: Genome-scale subcellular-location predictor for bacterial proteins-1

By 2D gel electrophoresis) which have a putative SPI-cleavage site motif in the C-region that follows the transmembrane helix H-region (see Fig. 1B). A sequence composition chart, made using WebLogo [47], based on multiple-sequence alignment of the H- and C-regions (see Fig. 1B) of the N-anchored and secreted protein sets. The red arrow indicates the cleavage position of true SPI-site motifs (see Figure 1B), and the green dashed arrow represents the corresponding position in N-anchored proteins that is not cleaved. The specificity of HMMs of different lengths containing the putative cleavage site A* = the Alanine after which cleavage takes place. Mod1: residues -9 to A*; Mod2: residues -11 to A*; Mod3: residues -14 to A*; Mod4: residues -8 to +3 of A*; Mod5: residues -13 to +10 of A*; Mod6: residues -8 to +17 of A*; Mod7: residues -3 to +10 of A*; Mod8: residues -3 to +17 of A*; Mod9: residues +1 to +25.<p><b>Copyright information:</b></p><p>Taken from "LocateP: Genome-scale subcellular-location predictor for bacterial proteins"</p><p>http://www.biomedcentral.com/1471-2105/9/173</p><p>BMC Bioinformatics 2008;9():173-173.</p><p>Published online 27 Mar 2008</p><p>PMCID:PMC2375117.</p><p></p

LocateP: Genome-scale subcellular-location predictor for bacterial proteins-2

by combining Tat-find v1.2 [91] and our Tat-specific HMMs (RR-HMM, CS-HMM). Bacteriocin-like proteins were identified using Bagel [149]. Secondly, Phobius [14], PrediSi [98], SignalP 3.0 [18] and TMHMM 2.0 [12] were combined to identify transmembrane regions. Those proteins without any predicted TM segments were considered intracellular, whereas those with TM segments were divided into multi-TM membrane proteins, N-anchored membrane proteins or secreted/released proteins (single N-terminal TM segment, possibly signal peptide), and C-anchored membrane proteins (signal peptide and single C-terminal TM segment). Thirdly, a sortase-substrate HMM [165] was used to distinguish LPxTG-type peptidoglycan-anchored proteins from C-anchored membrane proteins. Subsequently, signal peptidase type II (SPII) substrates were predicted by combining existing lipoprotein motif models [41, 157] and new lipoprotein HMMs. The remaining proteins were classified into the categories secreted/released or N-anchored membrane proteins. See Methods and additional file for more details. Abbreviation: A-S = Anchored-Secreted; TMS = TransMembrane Segment; SP = Signal Peptide; C/N-TM = C/N-terminally transmembrane anchored; LPxTG = LPxTG cell-wall anchored.<p><b>Copyright information:</b></p><p>Taken from "LocateP: Genome-scale subcellular-location predictor for bacterial proteins"</p><p>http://www.biomedcentral.com/1471-2105/9/173</p><p>BMC Bioinformatics 2008;9():173-173.</p><p>Published online 27 Mar 2008</p><p>PMCID:PMC2375117.</p><p></p

Additional file 12 of Environmental and maternal factors shaping tonsillar microbiota development in piglets

Additional file 12: Figure S6. Boxplots of different alpha diversity measures per timepoint

Impact of heat-treatment on germination and outgrowth of <i>B</i>. <i>cereus</i> ATCC14579 spores.

<p>(A) Relative change in OD₅₉₅ for untreated (circles) and heat-treated for 1 min at 95°C (squares) dormant spores was monitored in time in BHI broth at 30°C. Closed symbols indicate the sampling points selected for transcriptome analysis. The starting OD₅₉₅ was 0.15–0.2 (B) Microscopy analysis of samples taken before initiation of germination (t0) and at indicated time points (10 up to 150 min) thereafter.</p

Array expression ratios (log2 values) of candidate genes displaying specific upregulation during germination and outgrowth of heat-treated <i>B</i>. <i>cereus</i> ATCC14579 spores and verified by qPCR.

<p>False Discovery Rates below 0.05 are indicated in bold.</p