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CodonCode corporation phred software codoncode aligner
Phred Software Codoncode Aligner, 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/codoncode+phred/phred+program/10__1007_slash_s00300___009___0737___8-56-7-9
Average 90 stars, based on 1 article reviews
phred software codoncode aligner - by Bioz Stars, 2026-09
90/100 stars

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Related Articles

Sequencing:

Article Title: MicroRNAome
Article Snippet: .. Resulting sequence files were trimmed by using PHRED sequence analysis software (CodonCode, Dedham, Mass.), and 18- to 26-bp tags were extracted by using the SAGE2000 software package, which identifies the fragmenting enzyme site between tags, extracts intervening tags, and records them in a database. ..

Article Title: P13K pathway mutations in cancer
Article Snippet: Clones were sequenced using Big Dye terminators (ABI, Foster City, Calif.) and analyzed using a 384 capillary automated sequencing apparatus (Spectrumedix, State College, Pa.) or with a 96 capillary ABI 3700 instrument at Agencourt Biosciences (Beverly, Mass.). .. Digital karyotyping sequence files were trimmed using Phred sequence analysis software (CodonCode, Mass.) and 21 bp genomic tags were extracted using the SAGE2000 software package. ..

Article Title: Positive and negative selection on noncoding DNA close to protein-coding genes in wild house mice.
Article Snippet: CodonCode Aligner version 2.0.6 was used to analyze and detect variants (http:// www.codoncode.com/aligner/). .. We used Phred computer program as employed in CodonCode Aligner to assess sequence quality. ..

Article Title: Generation and Analysis of Expressed Sequence Tags from Olea europaea L.
Article Snippet: Automated sequencing was performed on an automated high-throughput pipeline using the ABI 3730 capillary sequencer (PE Applied Biosystems, Foster City, CA) at the Genome Sequencing Center, Washington University in St. Louis (WUSTL). .. EST sequences were trimmed of vector, adapter, and low-quality sequence by using Phred software [ , ] (CodonCode Crop., Dedham, MA.) ..

Software:

Article Title: MicroRNAome
Article Snippet: .. Resulting sequence files were trimmed by using PHRED sequence analysis software (CodonCode, Dedham, Mass.), and 18- to 26-bp tags were extracted by using the SAGE2000 software package, which identifies the fragmenting enzyme site between tags, extracts intervening tags, and records them in a database. ..

Article Title: P13K pathway mutations in cancer
Article Snippet: Clones were sequenced using Big Dye terminators (ABI, Foster City, Calif.) and analyzed using a 384 capillary automated sequencing apparatus (Spectrumedix, State College, Pa.) or with a 96 capillary ABI 3700 instrument at Agencourt Biosciences (Beverly, Mass.). .. Digital karyotyping sequence files were trimmed using Phred sequence analysis software (CodonCode, Mass.) and 21 bp genomic tags were extracted using the SAGE2000 software package. ..

Article Title: Complementary DNA library construction and expressed sequence tag analysis of an Arctic moss, Aulacomnium turgidum
Article Snippet: Unique physiological and metabolic properties of Arctic mosses are responsible for their acclimation to the inclement polar environment.. To perform transcriptome analysis of an Arctic moss species adapted to polar conditions, we constructed a complementary DNA (cDNA) library using total high-quality RNA extracted from the moss species Aulacomnium turgidum.. The library consisted of 1.81 £ 10 of independent clones with 97.41% of recombinants.

Article Title: Preparing and Analyzing Expressed Sequence Tags (ESTs) Library for the Mammary Tissue of Local Turkish Kivircik Sheep
Article Snippet: Automated sequencing was performed on an automated high-throughput pipeline using the ABI 3730 capillary sequencer (PE Applied Biosystems, Foster City, CA) at the Genome Sequencing Center, Washington University in St. Louis (WUSTL). .. For analysis of the raw EST data, the low-quality, adapter, and the vector sequences were removed with Phred software [ , ] (CodonCode Corp., Dedham, MA). ..

Article Title: Generation and Analysis of Expressed Sequence Tags from Olea europaea L.
Article Snippet: Automated sequencing was performed on an automated high-throughput pipeline using the ABI 3730 capillary sequencer (PE Applied Biosystems, Foster City, CA) at the Genome Sequencing Center, Washington University in St. Louis (WUSTL). .. EST sequences were trimmed of vector, adapter, and low-quality sequence by using Phred software [ , ] (CodonCode Crop., Dedham, MA.) ..

other:

Article Title: Human Gut Bacterial Communities Are Altered by Addition of Cruciferous Vegetables to a Controlled Fruit- and Vegetable-Free Diet
Article Snippet: 16S rRNA gene sequences were edited and assembled into consensus sequences using PHRED and PHRAP software packages (CodonCode) based on PHRAP quality scores of 20.

Article Title: Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences
Article Snippet: Sequences were assembled and the contig sequence was obtained by means of the Phred base-calling software and the Phrap assembly tool, which are available in the Codoncode aligner v.4.2.1 suite (Codoncode Corp. Dedham, MA, USA).

Plasmid Preparation:

Article Title: Complementary DNA library construction and expressed sequence tag analysis of an Arctic moss, Aulacomnium turgidum
Article Snippet: Unique physiological and metabolic properties of Arctic mosses are responsible for their acclimation to the inclement polar environment.. To perform transcriptome analysis of an Arctic moss species adapted to polar conditions, we constructed a complementary DNA (cDNA) library using total high-quality RNA extracted from the moss species Aulacomnium turgidum.. The library consisted of 1.81 £ 10 of independent clones with 97.41% of recombinants.

Article Title: Preparing and Analyzing Expressed Sequence Tags (ESTs) Library for the Mammary Tissue of Local Turkish Kivircik Sheep
Article Snippet: Automated sequencing was performed on an automated high-throughput pipeline using the ABI 3730 capillary sequencer (PE Applied Biosystems, Foster City, CA) at the Genome Sequencing Center, Washington University in St. Louis (WUSTL). .. For analysis of the raw EST data, the low-quality, adapter, and the vector sequences were removed with Phred software [ , ] (CodonCode Corp., Dedham, MA). ..

Article Title: Generation and Analysis of Expressed Sequence Tags from Olea europaea L.
Article Snippet: Automated sequencing was performed on an automated high-throughput pipeline using the ABI 3730 capillary sequencer (PE Applied Biosystems, Foster City, CA) at the Genome Sequencing Center, Washington University in St. Louis (WUSTL). .. EST sequences were trimmed of vector, adapter, and low-quality sequence by using Phred software [ , ] (CodonCode Crop., Dedham, MA.) ..



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