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SourceForge net blast extend repraze
Blast Extend Repraze, supplied by SourceForge net, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/basic+local+alignment+search+tool+software+program/blast+extend+repraze+ber/pmc04424289-23-6-10
Average 90 stars, based on 1 article reviews
blast extend repraze - by Bioz Stars, 2026-09
90/100 stars

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Related Articles

Sequencing:

Article Title: Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing
Article Snippet: Protein comparison and pairwise alignment For this step, the Blast-Extend-Repraze (BER) tool (http://sourceforge.net/projects/ber/) employs a two-step process that starts with a BLASTX search followed by a modified Smith-Waterman alignment.

Article Title: Identification of the Pangenome and Its Components in 14 Distinct Aggregatibacter actinomycetemcomitans Strains by Comparative Genomic Analysis
Article Snippet: Because our genome sequence data were produced using the 454 pyrosequencing technology, which tends to produce insertion/deletion (indel) nucleotide polymorphism in homopolymer stretches, protein-coding genes were further analyzed to identify putative frameshift mutations using BLAST Extend-Repraze ( http://ber.sourceforge.net/ ).

Article Title: Genome Sequence of Avery's Virulent Serotype 2 Strain D39 of Streptococcus pneumoniae and Comparison with That of Unencapsulated Laboratory Strain R6
Article Snippet: Blast-Extend-Repraze (BER; http://ber.sourceforge.net ) was used to search an internal nonidentical amino acid database constructed from all proteins available from GenBank ( http://www.ncbi.nlm.nih.gov ), UniProt ( http://www.pir2.uniprot.org/ ), and the Comprehensive Microbial Resource database ( http://www.tigr.org/CMR ).

Article Title: CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects – standard operating procedure, version 1.0
Article Snippet: Protein comparison and pairwise alignment For this step, the Blast-Extend-Repraze (BER) tool (http://sourceforge.net/projects/ber/) employs a two-step process that starts with a BLASTX search followed by a modified SmithWaterman alignment.

Article Title: Genome Sequences and Characterization of the Related Gordonia Phages GTE5 and GRU1 and Their Use as Potential Biocontrol Agents
Article Snippet: The BLAST X results were used as input for the BLAST-Extend-Repraze algorithm ( http://sourceforge.net/projects/ber/ ) to identify potential frameshifts or point mutations.

Produced:

Article Title: Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing
Article Snippet: Protein comparison and pairwise alignment For this step, the Blast-Extend-Repraze (BER) tool (http://sourceforge.net/projects/ber/) employs a two-step process that starts with a BLASTX search followed by a modified Smith-Waterman alignment.

Article Title: Identification of the Pangenome and Its Components in 14 Distinct Aggregatibacter actinomycetemcomitans Strains by Comparative Genomic Analysis
Article Snippet: Because our genome sequence data were produced using the 454 pyrosequencing technology, which tends to produce insertion/deletion (indel) nucleotide polymorphism in homopolymer stretches, protein-coding genes were further analyzed to identify putative frameshift mutations using BLAST Extend-Repraze ( http://ber.sourceforge.net/ ).

Article Title: Genome Sequence of Avery's Virulent Serotype 2 Strain D39 of Streptococcus pneumoniae and Comparison with That of Unencapsulated Laboratory Strain R6
Article Snippet: Blast-Extend-Repraze (BER; http://ber.sourceforge.net ) was used to search an internal nonidentical amino acid database constructed from all proteins available from GenBank ( http://www.ncbi.nlm.nih.gov ), UniProt ( http://www.pir2.uniprot.org/ ), and the Comprehensive Microbial Resource database ( http://www.tigr.org/CMR ).

Article Title: CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects – standard operating procedure, version 1.0
Article Snippet: Protein comparison and pairwise alignment For this step, the Blast-Extend-Repraze (BER) tool (http://sourceforge.net/projects/ber/) employs a two-step process that starts with a BLASTX search followed by a modified SmithWaterman alignment.

Article Title: Genome Sequences and Characterization of the Related Gordonia Phages GTE5 and GRU1 and Their Use as Potential Biocontrol Agents
Article Snippet: The BLAST X results were used as input for the BLAST-Extend-Repraze algorithm ( http://sourceforge.net/projects/ber/ ) to identify potential frameshifts or point mutations.

Comparison:

Article Title: Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing
Article Snippet: Protein comparison and pairwise alignment For this step, the Blast-Extend-Repraze (BER) tool (http://sourceforge.net/projects/ber/) employs a two-step process that starts with a BLASTX search followed by a modified Smith-Waterman alignment.

Article Title: Identification of the Pangenome and Its Components in 14 Distinct Aggregatibacter actinomycetemcomitans Strains by Comparative Genomic Analysis
Article Snippet: Because our genome sequence data were produced using the 454 pyrosequencing technology, which tends to produce insertion/deletion (indel) nucleotide polymorphism in homopolymer stretches, protein-coding genes were further analyzed to identify putative frameshift mutations using BLAST Extend-Repraze ( http://ber.sourceforge.net/ ).

Article Title: Genome Sequence of Avery's Virulent Serotype 2 Strain D39 of Streptococcus pneumoniae and Comparison with That of Unencapsulated Laboratory Strain R6
Article Snippet: Blast-Extend-Repraze (BER; http://ber.sourceforge.net ) was used to search an internal nonidentical amino acid database constructed from all proteins available from GenBank ( http://www.ncbi.nlm.nih.gov ), UniProt ( http://www.pir2.uniprot.org/ ), and the Comprehensive Microbial Resource database ( http://www.tigr.org/CMR ).

Article Title: CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects – standard operating procedure, version 1.0
Article Snippet: Protein comparison and pairwise alignment For this step, the Blast-Extend-Repraze (BER) tool (http://sourceforge.net/projects/ber/) employs a two-step process that starts with a BLASTX search followed by a modified SmithWaterman alignment.

Article Title: Genome Sequences and Characterization of the Related Gordonia Phages GTE5 and GRU1 and Their Use as Potential Biocontrol Agents
Article Snippet: The BLAST X results were used as input for the BLAST-Extend-Repraze algorithm ( http://sourceforge.net/projects/ber/ ) to identify potential frameshifts or point mutations.

Modification:

Article Title: Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing
Article Snippet: Protein comparison and pairwise alignment For this step, the Blast-Extend-Repraze (BER) tool (http://sourceforge.net/projects/ber/) employs a two-step process that starts with a BLASTX search followed by a modified Smith-Waterman alignment.

Article Title: Identification of the Pangenome and Its Components in 14 Distinct Aggregatibacter actinomycetemcomitans Strains by Comparative Genomic Analysis
Article Snippet: Because our genome sequence data were produced using the 454 pyrosequencing technology, which tends to produce insertion/deletion (indel) nucleotide polymorphism in homopolymer stretches, protein-coding genes were further analyzed to identify putative frameshift mutations using BLAST Extend-Repraze ( http://ber.sourceforge.net/ ).

Article Title: Genome Sequence of Avery's Virulent Serotype 2 Strain D39 of Streptococcus pneumoniae and Comparison with That of Unencapsulated Laboratory Strain R6
Article Snippet: Blast-Extend-Repraze (BER; http://ber.sourceforge.net ) was used to search an internal nonidentical amino acid database constructed from all proteins available from GenBank ( http://www.ncbi.nlm.nih.gov ), UniProt ( http://www.pir2.uniprot.org/ ), and the Comprehensive Microbial Resource database ( http://www.tigr.org/CMR ).

Article Title: CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects – standard operating procedure, version 1.0
Article Snippet: Protein comparison and pairwise alignment For this step, the Blast-Extend-Repraze (BER) tool (http://sourceforge.net/projects/ber/) employs a two-step process that starts with a BLASTX search followed by a modified SmithWaterman alignment.

Article Title: Genome Sequences and Characterization of the Related Gordonia Phages GTE5 and GRU1 and Their Use as Potential Biocontrol Agents
Article Snippet: The BLAST X results were used as input for the BLAST-Extend-Repraze algorithm ( http://sourceforge.net/projects/ber/ ) to identify potential frameshifts or point mutations.



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Image Search Results


A phylogenetic tree was generated using consensus hsp65 gene sequences of unidentified mycobacteria species obtained through Oxford Nanopore Technology amplicon-based deep sequencing. The tree illustrates slow-growing mycobacteria represented by red branches and rapid growers indicated by blue branches. Unidentified Mycobacterium species sequences from this study are labeled in red. Members of the Mycobacterium tuberculosis complex are highlighted in the yellow range. The scale bar expresses the average number of nucleotide substitutions per site. Circular markers signify the bootstrap support of branches within the tree. The isolates included in the construction of the phylogenetic tree are those represented by the reads listed in : 1H.1, 5H.1, 6H.1, 7H.1, 10H.1, 15H.1, 18H.1, 20H.1, 22H.1, 22H.2, 23H.1, 26H.1, 27H.1, and 27H.2.

Journal: IJID Regions

Article Title: Targeted deep sequencing of mycobacteria species from extrapulmonary sites not identified by routine line probe assays: A retrospective laboratory analysis of stored clinical cultures

doi: 10.1016/j.ijregi.2024.100464

Figure Lengend Snippet: A phylogenetic tree was generated using consensus hsp65 gene sequences of unidentified mycobacteria species obtained through Oxford Nanopore Technology amplicon-based deep sequencing. The tree illustrates slow-growing mycobacteria represented by red branches and rapid growers indicated by blue branches. Unidentified Mycobacterium species sequences from this study are labeled in red. Members of the Mycobacterium tuberculosis complex are highlighted in the yellow range. The scale bar expresses the average number of nucleotide substitutions per site. Circular markers signify the bootstrap support of branches within the tree. The isolates included in the construction of the phylogenetic tree are those represented by the reads listed in : 1H.1, 5H.1, 6H.1, 7H.1, 10H.1, 15H.1, 18H.1, 20H.1, 22H.1, 22H.2, 23H.1, 26H.1, 27H.1, and 27H.2.

Article Snippet: The consensus sequences were subjected to analysis through the National Centre for Biotechnology Information nucleotide Basic Local Alignment Search Tool software program [ ].

Techniques: Generated, Amplification, Sequencing, Labeling

A phylogenetic tree was generated using consensus rpoB gene sequences of unidentified mycobacteria species obtained through Oxford Nanopore Technology amplicon-based deep sequencing. The tree illustrates slow-growing mycobacteria represented by red branches and rapid growers indicated by blue branches. Unidentified Mycobacterium species sequences from the study are labeled in red. Members of the Mycobacterium tuberculosis complex are highlighted in the yellow range. The scale bar expresses the average number of nucleotide substitutions per site. Circular markers signify the bootstrap support of branches within the tree. The isolates included in the construction of the phylogenetic tree are those represented by the reads listed in : 1R.1, 2R.1, 6R.1, 8R.1, 9R.1, 10R.1, 10R.2, 10R.3, 10R.4, 10R.5, 15R.1, 16R.1, 18R.1, 20R.1, 21R.1, 22R.1, 23R.1, 24R.1, 26R.1, 27R.1, 28R.1.

Journal: IJID Regions

Article Title: Targeted deep sequencing of mycobacteria species from extrapulmonary sites not identified by routine line probe assays: A retrospective laboratory analysis of stored clinical cultures

doi: 10.1016/j.ijregi.2024.100464

Figure Lengend Snippet: A phylogenetic tree was generated using consensus rpoB gene sequences of unidentified mycobacteria species obtained through Oxford Nanopore Technology amplicon-based deep sequencing. The tree illustrates slow-growing mycobacteria represented by red branches and rapid growers indicated by blue branches. Unidentified Mycobacterium species sequences from the study are labeled in red. Members of the Mycobacterium tuberculosis complex are highlighted in the yellow range. The scale bar expresses the average number of nucleotide substitutions per site. Circular markers signify the bootstrap support of branches within the tree. The isolates included in the construction of the phylogenetic tree are those represented by the reads listed in : 1R.1, 2R.1, 6R.1, 8R.1, 9R.1, 10R.1, 10R.2, 10R.3, 10R.4, 10R.5, 15R.1, 16R.1, 18R.1, 20R.1, 21R.1, 22R.1, 23R.1, 24R.1, 26R.1, 27R.1, 28R.1.

Article Snippet: The consensus sequences were subjected to analysis through the National Centre for Biotechnology Information nucleotide Basic Local Alignment Search Tool software program [ ].

Techniques: Generated, Amplification, Sequencing, Labeling