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Structured Review

CodonCode corporation codoncode phred/phrap
Codoncode Phred/Phrap, 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/codoncode+phred+phrap/pmc03595216-151-9-8
Average 90 stars, based on 1 article reviews
codoncode phred/phrap - by Bioz Stars, 2026-09
90/100 stars

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Related Articles

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), PHRAP (www.codoncode. com), Consensus Maker I (http://hiv-web.lanl.gov) and Consensus Maker II (http://web.comlab.ox.ac.uk/), all that have their relative advantages and disadvantages. ..

Sequencing:

Article Title: Identification of Cathepsin B as a Mediator of Neuronal Death Induced by Aβ-activated Microglial Cells Using a Functional Genomics Approach
Article Snippet: .. Sequence analysis was performed using Phrap (CodonCode, Dedham, MA), and a comprehensive homology analysis was conducted using a Blast algorithm against the RefSeq (NCBI) data base on accelerated hardware (TimeLogic, Reno, NV). ..

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 [ ], Phrap and Cross_match [ , ], were used with Codoncode InterPhace ( http://www.codoncode.com ). ..

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 Phrap (CodonCode, Dedham, Massachusetts, United States), and any gaps or regions of poor coverage were re-sequenced using primer-directed sequencing directly from the original PCR product using Big-Dye primer chemistry (Applied Biosystems). ..

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 Phrap (CodonCode, Dedham, Massachusetts, United States), and any gaps or regions of poor coverage were re-sequenced using primer-directed sequencing directly from the original PCR product using Big-Dye primer chemistry (Applied Biosystems). ..



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