CLUSS: Clustering of protein sequences based on a new similarity measure-0

<p><b>Copyright information:</b></p><p>Taken from "CLUSS: Clustering of protein sequences based on a new similarity measure"</p><p>http://www.biomedcentral.com/1471-2105/8/286</p><p>BMC Bioinformatics 2007;8():286-286.</p><p>Published online 4 Aug 2007</p><p>PMCID:PMC1976428.</p><p></p>he 1000 randomly generated subsets from the COG database. As shown, the obtained results are in good concordance with the functional reference characterization of COG. The average of the quality measure of the 1000 clusterings is equal to with a standard deviation equal to . More than of the 1000 clusterings obtained a quality measure superior to , and more than of the clusterings obtained a quality measure superior to . The minimum value of the quality measure is and the maximum value is

Examples of visualizations of tandem repeats in human chromosome 21 [GenBank: NC_000021.9].

<p>The scale represents a segment of 20 nucleotides. A: microsatellite consisting of CA repeats (nucleotide coordinates 6565371–6566350); B: GGAAT tandem repeats, also known as DNA satellite III (7259491–7260680); C: imperfect [TCTA][TCTG] 4bp repeat in the D21S11 locus included in CODIS database (19181961–19182170). D: 171-base pairs repeat, also known as alphoid DNA satellite or α-satellite (7265231–7269080).</p

DDV generator dependencies and visualized DNA Data interface files.

<p>DDV is a C# application that generates sequence specific files for each DNA dataset, as well as the shared CSS, JavaScript, and PHP files in the output folder. The included civetweb serves the PHP files when the user is viewing the visualized interface on a local PC.</p

Visualization of the 16.5 kb-terminal segments of the <i>Streptomyces davawensis</i> JCM 4913 chromosome [GenBank: HE971709].

<p>The segments are parts of the 33.3 kb LTIRs of this genome. A: image of the left end of the chromosome; B: 180°-rotated image of the right end of the chromosome.</p

CLUSS: Clustering of protein sequences based on a new similarity measure-1

<p><b>Copyright information:</b></p><p>Taken from "CLUSS: Clustering of protein sequences based on a new similarity measure"</p><p>http://www.biomedcentral.com/1471-2105/8/286</p><p>BMC Bioinformatics 2007;8():286-286.</p><p>Published online 4 Aug 2007</p><p>PMCID:PMC1976428.</p><p></p>clustering results obtained on six randomly generated subsets: SS1, red; SS2, blue; SS3, green; SS4, yellow; SS5, gray; SS6, amber

CLUSS: Clustering of protein sequences based on a new similarity measure-6

<p><b>Copyright information:</b></p><p>Taken from "CLUSS: Clustering of protein sequences based on a new similarity measure"</p><p>http://www.biomedcentral.com/1471-2105/8/286</p><p>BMC Bioinformatics 2007;8():286-286.</p><p>Published online 4 Aug 2007</p><p>PMCID:PMC1976428.</p><p></p>ank: ), GaA(GenBank: ), GaK(GenBank: ), GaC(GenBank: ), GaEcl(DDBJ: ), GaL(GenBank: ), GIC(GenBank: ), GIE(GenBank: ), GIH(GenBank: ), GIL(GenBank: ), GIM(GenBank: ), GIF(GenBank: ), GIS(GenBank: ), MaA(EMBL: ), MaB(GenBank: ), MaC(GenBank: ), MaH(GenBank: ), MaM(GenBank: ), MaT(EMBL: ), CsAo(GenBank: ), CsS(DDBJ: ), CsG(NCBI: XM_382490), CsM(NCBI: XP_369600), CsN(NCBI: XP_331434), CsAn(GenBank: ), CsH(DDBJ: ), CsE(NCBI: XP_746417), UnA(GenBank: ), UnBv(GenBank: ), UnBc(NCBI: ZP_00425692), UnBm(GenBank: ), UnBp(NCBI: YP_107240), UnR(GenBank: )

Ribosomal RNA gene clusters.

<p>Zoomed-in fragments of the visualization of the <i>Streptomyces coelicolor</i> A3(2) [GenBank: NC_003888] linear chromosome showing the <i>rrnB</i> and <i>rrnA</i> ribosomal gene clusters (coordinates 1916451 to 1921599 and 4530650 to 4535576). Arrows indicate the limits of each cluster. Empty arrows indicate the direction of chromosomal DNA replication fork movement and the direction of rRNA genes transcription.</p

Screenshot of generated interface for visualized data set: <i>Frankia</i> sp. CcI3 genome [GenBank:NC_007777], 5433628 bp.

<p>Screenshot taken after computing nucleotide density for the whole sequence, zooming in, generating GC-Skew plot for the sequence, and selecting a sequence fragment at bp 2882288. The interface includes a scale bar (bottom left of Deep Zoom viewer) shown in bp units, and a viewport navigator (top right of Deep Zoom viewer) that shows zoom position and can also be used for panning.</p

Visualization of the <i>Clostridium difficile</i> 630 chromosome [GenBank: NC_009089].

<p>Segments corresponding to the seven known conjugative transposons are indicated by brackets. 1: CTn1; 2: CTn2; 3: CTn3, also known as Tn<i>5397</i>; 4: CTn 4; 5: CTn5; 6: CTn6; 7:CTn7.</p

CLUSS: Clustering of protein sequences based on a new similarity measure-4

<p><b>Copyright information:</b></p><p>Taken from "CLUSS: Clustering of protein sequences based on a new similarity measure"</p><p>http://www.biomedcentral.com/1471-2105/8/286</p><p>BMC Bioinformatics 2007;8():286-286.</p><p>Published online 4 Aug 2007</p><p>PMCID:PMC1976428.</p><p></p> (DDBJ: , DDBJ: ) "" and (GenBank: , DDBJ: ) "" activities. Subfamily SF_8 also includes closely related plant enzymes and bacterial enzymes produced by members of the genus Xanthomonas, including several plant pathogens