alignment software (CodonCode corporation)

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CodonCode corporation alignment software
Alignment Software, 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/phred+software+codoncode+aligner/alignment+software/pmc03001726-207-1-1
Average 90 stars, based on 1 article reviews

alignment software - by Bioz Stars, 2026-10

90/100 stars

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Software:

Article Title: Pyrosequencing Reveals Restricted Patterns of CD8 + T Cell Escape-Associated Compensatory Mutations in Simian Immunodeficiency Virus
Article Snippet: Within Roche AVA, flowgram reads were aligned to the reference SIVmac239 sequence (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"M33262","term_id":"334647","term_text":"M33262"}} M33262 ), and then identical read results were assembled into groups. .. Manual editing was performed using CodonCode alignment software (CodonCode Corp., Dedham, MA) only when homopolymeric regions differed by ±1 nucleotide and resulted in frameshifts. .. Improved base-calling using Roche AVA software compensates for base addition artifacts in homopolymeric regions, and manual editing was kept to a minimum.

Article Title: Signatures of selection in loci governing major colour patterns in Heliconius butterflies and related species
Article Snippet: .. Using CodonCode alignment software, 454 consensus sequences and raw reads of each species or race for each gene were aligned against the BAC sequence to ensure that the transcripts were from the genes of interest. ..

Article Title: Pyrosequencing Reveals Restricted Patterns of CD8+ T Cell Escape-Associated Compensatory Mutations in Simian Immunodeficiency Virus
Article Snippet: Within Roche AVA, flowgram reads were aligned to the reference SIVmac239 sequence (GenBank accession no. M33262), and then identical read results were assembled into groups. .. Manual editing was performed using CodonCode alignment software (CodonCode Corp., Dedham, MA) only when homopolymeric regions differed by 1 nucleotide and resulted in frameshifts. .. Improved base-calling using Roche AVA software compensates for base addition artifacts in homopolymeric regions, and manual editing was kept to a minimum.

BAC Assay:

Sequencing:

other:

Article Title: Artemisinin and partner drug resistance markers in Plasmodium falciparum from Tanzanian paediatric malaria patients, 2016-2022.
Article Snippet: Amplicons were subsequently Sanger-sequenced (Eurofins Genomics, Germany), and aligned to 3D7 reference sequences (plasmoDB.org) using CodonCode Version 9.0.1.

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