sequence similarity search [basic local alignment search tool nucleotide (blast) search] Search Results


ncbi genbank blast similarity search program  (Biotechnology Information)
86
Biotechnology Information ncbi genbank blast similarity search program
Ncbi Genbank Blast Similarity Search Program, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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sequence similarity networks  (Baier labs)
90
Baier labs sequence similarity networks
Sequence Similarity Networks, supplied by Baier labs, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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vector nti software  (InforMax Inc)
90
InforMax Inc vector nti software
(A) Alignment of the promoter region of S. gordonii fruR with the fruR homologs in S. pneumoniae (accession no. NP345362), S. mitis, S. mutans (accession no. NC004350), S. pyogenes (accession no. 002737), and S. agalactiae (accession no. NC004116) determined by using the AlignX program in the Vector <t>NTI</t> software (Informax). Streptococcal sequences without accession numbers were obtained from the unfinished microbial genome database (www.ncbi.nlm.nih.gov). Nucleotides that are identical and conserved are indicated by dark grey and light grey backgrounds, respectively, and start codons are enclosed in boxes. In S. gordonii, direct repeat regions (DR) are indicated by horizontal arrows, while the CRE, putative ribosome binding site (rbs), putative −35, and putative −10 regions are underlined. (B) Phylogenetic tree of S. gordonii FruR and other bacterial sugar PTS regulatory proteins. The phylogenetic relatedness dendrogram was constructed on the basis of amino <t>acid</t> <t>sequence</t> similarities by using the AlignX program in the Vector NTI software (Informax Inc.), which utilizes the neighbor-joining algorithm (32). The reliability of the topology was estimated by performing 100 bootstrap trials, and the bootstrap values are expressed in percentages at branch points (www.genebee.msu.su). Accession numbers follow the species names, and sequences without accession numbers were obtained from the unfinished microbial genome sequence database (www.ncbi.nlm.nih.gov).
Vector Nti Software, supplied by InforMax Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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sequence analysis software genetyx-sv/rc  (GENETYX CORPORATION)
90
GENETYX CORPORATION sequence analysis software genetyx-sv/rc
(A) Alignment of the promoter region of S. gordonii fruR with the fruR homologs in S. pneumoniae (accession no. NP345362), S. mitis, S. mutans (accession no. NC004350), S. pyogenes (accession no. 002737), and S. agalactiae (accession no. NC004116) determined by using the AlignX program in the Vector <t>NTI</t> software (Informax). Streptococcal sequences without accession numbers were obtained from the unfinished microbial genome database (www.ncbi.nlm.nih.gov). Nucleotides that are identical and conserved are indicated by dark grey and light grey backgrounds, respectively, and start codons are enclosed in boxes. In S. gordonii, direct repeat regions (DR) are indicated by horizontal arrows, while the CRE, putative ribosome binding site (rbs), putative −35, and putative −10 regions are underlined. (B) Phylogenetic tree of S. gordonii FruR and other bacterial sugar PTS regulatory proteins. The phylogenetic relatedness dendrogram was constructed on the basis of amino <t>acid</t> <t>sequence</t> similarities by using the AlignX program in the Vector NTI software (Informax Inc.), which utilizes the neighbor-joining algorithm (32). The reliability of the topology was estimated by performing 100 bootstrap trials, and the bootstrap values are expressed in percentages at branch points (www.genebee.msu.su). Accession numbers follow the species names, and sequences without accession numbers were obtained from the unfinished microbial genome sequence database (www.ncbi.nlm.nih.gov).
Sequence Analysis Software Genetyx Sv/Rc, supplied by GENETYX CORPORATION, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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software megalign option  (DNASTAR)
99
DNASTAR software megalign option
(A) Alignment of the promoter region of S. gordonii fruR with the fruR homologs in S. pneumoniae (accession no. NP345362), S. mitis, S. mutans (accession no. NC004350), S. pyogenes (accession no. 002737), and S. agalactiae (accession no. NC004116) determined by using the AlignX program in the Vector <t>NTI</t> software (Informax). Streptococcal sequences without accession numbers were obtained from the unfinished microbial genome database (www.ncbi.nlm.nih.gov). Nucleotides that are identical and conserved are indicated by dark grey and light grey backgrounds, respectively, and start codons are enclosed in boxes. In S. gordonii, direct repeat regions (DR) are indicated by horizontal arrows, while the CRE, putative ribosome binding site (rbs), putative −35, and putative −10 regions are underlined. (B) Phylogenetic tree of S. gordonii FruR and other bacterial sugar PTS regulatory proteins. The phylogenetic relatedness dendrogram was constructed on the basis of amino <t>acid</t> <t>sequence</t> similarities by using the AlignX program in the Vector NTI software (Informax Inc.), which utilizes the neighbor-joining algorithm (32). The reliability of the topology was estimated by performing 100 bootstrap trials, and the bootstrap values are expressed in percentages at branch points (www.genebee.msu.su). Accession numbers follow the species names, and sequences without accession numbers were obtained from the unfinished microbial genome sequence database (www.ncbi.nlm.nih.gov).
Software Megalign Option, supplied by DNASTAR, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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basic local alignment search tool blast comparison  (Biotechnology Information)
86
Biotechnology Information basic local alignment search tool blast comparison
(A) Alignment of the promoter region of S. gordonii fruR with the fruR homologs in S. pneumoniae (accession no. NP345362), S. mitis, S. mutans (accession no. NC004350), S. pyogenes (accession no. 002737), and S. agalactiae (accession no. NC004116) determined by using the AlignX program in the Vector <t>NTI</t> software (Informax). Streptococcal sequences without accession numbers were obtained from the unfinished microbial genome database (www.ncbi.nlm.nih.gov). Nucleotides that are identical and conserved are indicated by dark grey and light grey backgrounds, respectively, and start codons are enclosed in boxes. In S. gordonii, direct repeat regions (DR) are indicated by horizontal arrows, while the CRE, putative ribosome binding site (rbs), putative −35, and putative −10 regions are underlined. (B) Phylogenetic tree of S. gordonii FruR and other bacterial sugar PTS regulatory proteins. The phylogenetic relatedness dendrogram was constructed on the basis of amino <t>acid</t> <t>sequence</t> similarities by using the AlignX program in the Vector NTI software (Informax Inc.), which utilizes the neighbor-joining algorithm (32). The reliability of the topology was estimated by performing 100 bootstrap trials, and the bootstrap values are expressed in percentages at branch points (www.genebee.msu.su). Accession numbers follow the species names, and sequences without accession numbers were obtained from the unfinished microbial genome sequence database (www.ncbi.nlm.nih.gov).
Basic Local Alignment Search Tool Blast Comparison, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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blastn  (Biotechnology Information)
86
Biotechnology Information blastn
(A) Alignment of the promoter region of S. gordonii fruR with the fruR homologs in S. pneumoniae (accession no. NP345362), S. mitis, S. mutans (accession no. NC004350), S. pyogenes (accession no. 002737), and S. agalactiae (accession no. NC004116) determined by using the AlignX program in the Vector <t>NTI</t> software (Informax). Streptococcal sequences without accession numbers were obtained from the unfinished microbial genome database (www.ncbi.nlm.nih.gov). Nucleotides that are identical and conserved are indicated by dark grey and light grey backgrounds, respectively, and start codons are enclosed in boxes. In S. gordonii, direct repeat regions (DR) are indicated by horizontal arrows, while the CRE, putative ribosome binding site (rbs), putative −35, and putative −10 regions are underlined. (B) Phylogenetic tree of S. gordonii FruR and other bacterial sugar PTS regulatory proteins. The phylogenetic relatedness dendrogram was constructed on the basis of amino <t>acid</t> <t>sequence</t> similarities by using the AlignX program in the Vector NTI software (Informax Inc.), which utilizes the neighbor-joining algorithm (32). The reliability of the topology was estimated by performing 100 bootstrap trials, and the bootstrap values are expressed in percentages at branch points (www.genebee.msu.su). Accession numbers follow the species names, and sequences without accession numbers were obtained from the unfinished microbial genome sequence database (www.ncbi.nlm.nih.gov).
Blastn, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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multiple sequence analysis clustalw software  (MacVector inc)
90
MacVector inc multiple sequence analysis clustalw software
(A) Alignment of the promoter region of S. gordonii fruR with the fruR homologs in S. pneumoniae (accession no. NP345362), S. mitis, S. mutans (accession no. NC004350), S. pyogenes (accession no. 002737), and S. agalactiae (accession no. NC004116) determined by using the AlignX program in the Vector <t>NTI</t> software (Informax). Streptococcal sequences without accession numbers were obtained from the unfinished microbial genome database (www.ncbi.nlm.nih.gov). Nucleotides that are identical and conserved are indicated by dark grey and light grey backgrounds, respectively, and start codons are enclosed in boxes. In S. gordonii, direct repeat regions (DR) are indicated by horizontal arrows, while the CRE, putative ribosome binding site (rbs), putative −35, and putative −10 regions are underlined. (B) Phylogenetic tree of S. gordonii FruR and other bacterial sugar PTS regulatory proteins. The phylogenetic relatedness dendrogram was constructed on the basis of amino <t>acid</t> <t>sequence</t> similarities by using the AlignX program in the Vector NTI software (Informax Inc.), which utilizes the neighbor-joining algorithm (32). The reliability of the topology was estimated by performing 100 bootstrap trials, and the bootstrap values are expressed in percentages at branch points (www.genebee.msu.su). Accession numbers follow the species names, and sequences without accession numbers were obtained from the unfinished microbial genome sequence database (www.ncbi.nlm.nih.gov).
Multiple Sequence Analysis Clustalw Software, supplied by MacVector inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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tblastn program  (DuPont de Nemours)
90
DuPont de Nemours tblastn program
(A) Alignment of the promoter region of S. gordonii fruR with the fruR homologs in S. pneumoniae (accession no. NP345362), S. mitis, S. mutans (accession no. NC004350), S. pyogenes (accession no. 002737), and S. agalactiae (accession no. NC004116) determined by using the AlignX program in the Vector <t>NTI</t> software (Informax). Streptococcal sequences without accession numbers were obtained from the unfinished microbial genome database (www.ncbi.nlm.nih.gov). Nucleotides that are identical and conserved are indicated by dark grey and light grey backgrounds, respectively, and start codons are enclosed in boxes. In S. gordonii, direct repeat regions (DR) are indicated by horizontal arrows, while the CRE, putative ribosome binding site (rbs), putative −35, and putative −10 regions are underlined. (B) Phylogenetic tree of S. gordonii FruR and other bacterial sugar PTS regulatory proteins. The phylogenetic relatedness dendrogram was constructed on the basis of amino <t>acid</t> <t>sequence</t> similarities by using the AlignX program in the Vector NTI software (Informax Inc.), which utilizes the neighbor-joining algorithm (32). The reliability of the topology was estimated by performing 100 bootstrap trials, and the bootstrap values are expressed in percentages at branch points (www.genebee.msu.su). Accession numbers follow the species names, and sequences without accession numbers were obtained from the unfinished microbial genome sequence database (www.ncbi.nlm.nih.gov).
Tblastn Program, supplied by DuPont de Nemours, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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tools for sequence similarity searches  (OnRamp BioInformatics)
90
OnRamp BioInformatics tools for sequence similarity searches
(A) Alignment of the promoter region of S. gordonii fruR with the fruR homologs in S. pneumoniae (accession no. NP345362), S. mitis, S. mutans (accession no. NC004350), S. pyogenes (accession no. 002737), and S. agalactiae (accession no. NC004116) determined by using the AlignX program in the Vector <t>NTI</t> software (Informax). Streptococcal sequences without accession numbers were obtained from the unfinished microbial genome database (www.ncbi.nlm.nih.gov). Nucleotides that are identical and conserved are indicated by dark grey and light grey backgrounds, respectively, and start codons are enclosed in boxes. In S. gordonii, direct repeat regions (DR) are indicated by horizontal arrows, while the CRE, putative ribosome binding site (rbs), putative −35, and putative −10 regions are underlined. (B) Phylogenetic tree of S. gordonii FruR and other bacterial sugar PTS regulatory proteins. The phylogenetic relatedness dendrogram was constructed on the basis of amino <t>acid</t> <t>sequence</t> similarities by using the AlignX program in the Vector NTI software (Informax Inc.), which utilizes the neighbor-joining algorithm (32). The reliability of the topology was estimated by performing 100 bootstrap trials, and the bootstrap values are expressed in percentages at branch points (www.genebee.msu.su). Accession numbers follow the species names, and sequences without accession numbers were obtained from the unfinished microbial genome sequence database (www.ncbi.nlm.nih.gov).
Tools For Sequence Similarity Searches, supplied by OnRamp BioInformatics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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dnaman software  (Lynnon corporation)
90
Lynnon corporation dnaman software
(A) Alignment of the promoter region of S. gordonii fruR with the fruR homologs in S. pneumoniae (accession no. NP345362), S. mitis, S. mutans (accession no. NC004350), S. pyogenes (accession no. 002737), and S. agalactiae (accession no. NC004116) determined by using the AlignX program in the Vector <t>NTI</t> software (Informax). Streptococcal sequences without accession numbers were obtained from the unfinished microbial genome database (www.ncbi.nlm.nih.gov). Nucleotides that are identical and conserved are indicated by dark grey and light grey backgrounds, respectively, and start codons are enclosed in boxes. In S. gordonii, direct repeat regions (DR) are indicated by horizontal arrows, while the CRE, putative ribosome binding site (rbs), putative −35, and putative −10 regions are underlined. (B) Phylogenetic tree of S. gordonii FruR and other bacterial sugar PTS regulatory proteins. The phylogenetic relatedness dendrogram was constructed on the basis of amino <t>acid</t> <t>sequence</t> similarities by using the AlignX program in the Vector NTI software (Informax Inc.), which utilizes the neighbor-joining algorithm (32). The reliability of the topology was estimated by performing 100 bootstrap trials, and the bootstrap values are expressed in percentages at branch points (www.genebee.msu.su). Accession numbers follow the species names, and sequences without accession numbers were obtained from the unfinished microbial genome sequence database (www.ncbi.nlm.nih.gov).
Dnaman Software, supplied by Lynnon corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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blast  (Biotechnology Information)
86
Biotechnology Information blast
(A) Alignment of the promoter region of S. gordonii fruR with the fruR homologs in S. pneumoniae (accession no. NP345362), S. mitis, S. mutans (accession no. NC004350), S. pyogenes (accession no. 002737), and S. agalactiae (accession no. NC004116) determined by using the AlignX program in the Vector <t>NTI</t> software (Informax). Streptococcal sequences without accession numbers were obtained from the unfinished microbial genome database (www.ncbi.nlm.nih.gov). Nucleotides that are identical and conserved are indicated by dark grey and light grey backgrounds, respectively, and start codons are enclosed in boxes. In S. gordonii, direct repeat regions (DR) are indicated by horizontal arrows, while the CRE, putative ribosome binding site (rbs), putative −35, and putative −10 regions are underlined. (B) Phylogenetic tree of S. gordonii FruR and other bacterial sugar PTS regulatory proteins. The phylogenetic relatedness dendrogram was constructed on the basis of amino <t>acid</t> <t>sequence</t> similarities by using the AlignX program in the Vector NTI software (Informax Inc.), which utilizes the neighbor-joining algorithm (32). The reliability of the topology was estimated by performing 100 bootstrap trials, and the bootstrap values are expressed in percentages at branch points (www.genebee.msu.su). Accession numbers follow the species names, and sequences without accession numbers were obtained from the unfinished microbial genome sequence database (www.ncbi.nlm.nih.gov).
Blast, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


(A) Alignment of the promoter region of S. gordonii fruR with the fruR homologs in S. pneumoniae (accession no. NP345362), S. mitis, S. mutans (accession no. NC004350), S. pyogenes (accession no. 002737), and S. agalactiae (accession no. NC004116) determined by using the AlignX program in the Vector NTI software (Informax). Streptococcal sequences without accession numbers were obtained from the unfinished microbial genome database (www.ncbi.nlm.nih.gov). Nucleotides that are identical and conserved are indicated by dark grey and light grey backgrounds, respectively, and start codons are enclosed in boxes. In S. gordonii, direct repeat regions (DR) are indicated by horizontal arrows, while the CRE, putative ribosome binding site (rbs), putative −35, and putative −10 regions are underlined. (B) Phylogenetic tree of S. gordonii FruR and other bacterial sugar PTS regulatory proteins. The phylogenetic relatedness dendrogram was constructed on the basis of amino acid sequence similarities by using the AlignX program in the Vector NTI software (Informax Inc.), which utilizes the neighbor-joining algorithm (32). The reliability of the topology was estimated by performing 100 bootstrap trials, and the bootstrap values are expressed in percentages at branch points (www.genebee.msu.su). Accession numbers follow the species names, and sequences without accession numbers were obtained from the unfinished microbial genome sequence database (www.ncbi.nlm.nih.gov).

Journal:

Article Title: Involvement of an Inducible Fructose Phosphotransferase Operon in Streptococcus gordonii Biofilm Formation

doi: 10.1128/JB.185.21.6241-6254.2003

Figure Lengend Snippet: (A) Alignment of the promoter region of S. gordonii fruR with the fruR homologs in S. pneumoniae (accession no. NP345362), S. mitis, S. mutans (accession no. NC004350), S. pyogenes (accession no. 002737), and S. agalactiae (accession no. NC004116) determined by using the AlignX program in the Vector NTI software (Informax). Streptococcal sequences without accession numbers were obtained from the unfinished microbial genome database (www.ncbi.nlm.nih.gov). Nucleotides that are identical and conserved are indicated by dark grey and light grey backgrounds, respectively, and start codons are enclosed in boxes. In S. gordonii, direct repeat regions (DR) are indicated by horizontal arrows, while the CRE, putative ribosome binding site (rbs), putative −35, and putative −10 regions are underlined. (B) Phylogenetic tree of S. gordonii FruR and other bacterial sugar PTS regulatory proteins. The phylogenetic relatedness dendrogram was constructed on the basis of amino acid sequence similarities by using the AlignX program in the Vector NTI software (Informax Inc.), which utilizes the neighbor-joining algorithm (32). The reliability of the topology was estimated by performing 100 bootstrap trials, and the bootstrap values are expressed in percentages at branch points (www.genebee.msu.su). Accession numbers follow the species names, and sequences without accession numbers were obtained from the unfinished microbial genome sequence database (www.ncbi.nlm.nih.gov).

Article Snippet: The phylogenetic relatedness dendrogram was constructed on the basis of amino acid sequence similarities by using the AlignX program in the Vector NTI software (Informax Inc.), which utilizes the neighbor-joining algorithm ( 32 ).

Techniques: Plasmid Preparation, Software, Binding Assay, Construct, Sequencing