phrap program (CodonCode corporation)
90
Structured Review
CodonCode corporation
phrap program
Phrap Program, supplied by CodonCode corporation, 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/phrap/phrap/pmc01975466-199-27-32
Average 90 stars, based on 1 article reviews
Phrap Program, supplied by CodonCode corporation, 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/phrap/phrap/pmc01975466-199-27-32
Average 90 stars, based on 1 article reviews
phrap program - by Bioz Stars,
2026-11
90/100 stars
Images
1) Product Images from "Persistent Infection and Promiscuous Recombination of Multiple Genotypes of an RNA Virus within a Single Host Generate Extensive Diversity"
Article Title: Persistent Infection and Promiscuous Recombination of Multiple Genotypes of an RNA Virus within a Single Host Generate Extensive Diversity
Journal: PLoS ONE
doi: 10.1371/journal.pone.0000917
Figure Legend Snippet: Unrooted, consensus phylogenetic trees were obtained from 2,000,000 generations of the Markov chain Monte Carlo simulation in Bayesian analysis using a general time-reversal model of nucleotide substitution . The number above each branch indicates the Bayesian posterior probability. The scale bars represent 0.1 expected substitutions per site. Branch lengths are proportional to evolutionary distance. Sequences were aligned using ClustalX and subsequently manually aligned prior to the Bayesian phylogenetic analysis. A, Known CTV genomes and CTV genomes assembled from resequencing analysis of FS2-2 (highlighted orange). The suffix at the end of fs2_2 distinguishes multiple genotypes in the isolate and also indicates the anchor sequence from which the consensus contig was generated by the Phrap program. B, the 5′ proximal 1 kb, and C, p33-coding region of CTV genomes obtained by direct sequencing of RT-PCR clones. In both B and C, Bayesian posterior probability and clones with identical sequences were omitted for clarity. Recombinant sequences are highlighted in green.
Techniques Used: Sequencing, Generated, Reverse Transcription Polymerase Chain Reaction, Clone Assay, Recombinant
Related Articles
Sequencing:Article Title: Persistent Infection and Promiscuous Recombination of Multiple Genotypes of an RNA Virus within a Single Host Generate Extensive Diversity Article Snippet: Base calls were made using the ABACUS (adaptive background genotype calling scheme) algorithm . .. Sequence fragments and the associated quality scores generated by GDAS were converted into fasta-format files and used to assemble full and partial CTV genomic contigs using the Article Title: Identification of stress-responsive genes in Ammopiptanthus mongolicus using ESTs generated from cold- and drought-stressed seedlings Article Snippet: White clones grown on screening LB medium (Amp/IPTG/X-Gal) were recovered by random colony selection and inserts were sequenced from the 5′ end using T7 primer and an ABI 3730 capillary sequencer in Shanghai United Gene Institute of China. .. Standard sequence processing tools, Phred [ ], Article Title: Genetic Analysis of the Capsular Biosynthetic Locus from All 90 Pneumococcal Serotypes Article Snippet: Clones from each library were sequenced from each end using Big-Dye terminator chemistry (Applied Biosystems, Foster City, California, United States) on ABI3730 sequencing machines, to give an average of 8- to 10-fold coverage of each product. .. These reads were assembled with Generated:Article Title: Persistent Infection and Promiscuous Recombination of Multiple Genotypes of an RNA Virus within a Single Host Generate Extensive Diversity Article Snippet: Base calls were made using the ABACUS (adaptive background genotype calling scheme) algorithm . .. Sequence fragments and the associated quality scores generated by GDAS were converted into fasta-format files and used to assemble full and partial CTV genomic contigs using the Software:Article Title: ProteinParser--a community based tool for the generation of a detailed protein consensus and FASTA output. Article Snippet: .. Specific consensus generating software is both non- and commercially available, PRETTY (www.accelrys.com), Vector NTI (http://www.invitrogen.com), Polymerase Chain Reaction:Article Title: Genetic Analysis of the Capsular Biosynthetic Locus from All 90 Pneumococcal Serotypes Article Snippet: Clones from each library were sequenced from each end using Big-Dye terminator chemistry (Applied Biosystems, Foster City, California, United States) on ABI3730 sequencing machines, to give an average of 8- to 10-fold coverage of each product. .. These reads were assembled with Hybridization:Article Title: Persistent Infection and Promiscuous Recombination of Multiple Genotypes of an RNA Virus within a Single Host Generate Extensive Diversity Article Snippet: .. Each nucleotide in these fragments was assigned a quality score by GSEQ, on the basis of differential hybridization of perfect-matches and mismatches in the sense and antisense quartets as well as on the basis of and partial CTV genomic contigs using the |