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Unigene computer programs phred and cap3
Computer Programs Phred And Cap3, supplied by Unigene, 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/cap3+computer+program/cap3+software/pm16121253-4-12-16
Average 90 stars, based on 1 article reviews
computer programs phred and cap3 - by Bioz Stars, 2026-10
90/100 stars

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Related Articles

Software:

Article Title: Generation of a wheat leaf rust, Puccinia triticina, EST database from stage-specific cDNA libraries.
Article Snippet: .. The extent of redundancy for each library preparation was ascertained using the CAP3 software (Huang and Madan, 1999), which was also used to compile the unigene set (default settings: overlap length cutoff > 30, identity > 75%, gap penalty factor of 6; varying these parameters experimentally did not yield significant changes in the unigene set). ..

Article Title: Whole-transcriptome analysis of differentially expressed genes in the ray florets and disc florets of Chrysanthemum morifolium
Article Snippet: .. The intra-scaffold gaps were filled and a non-redundant unigene set was constructed from all three assembled datasets using CAP3 software [ ]. ..

Article Title: Transcriptome Analysis of Syringa oblata Lindl. Inflorescence Identifies Genes Associated with Pigment Biosynthesis and Scent Metabolism
Article Snippet: The spliced sequence was called the primary unigene. .. The primary unigene was further assembled to the final unigene with the CAP3 EST software[ ]. ..

Article Title: Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome.
Article Snippet: The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus.. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant.. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins.

Article Title: Temporal Gene Expression Profiling of the Wheat Leaf Rust Pathosystem Using cDNA Microarray Reveals Differences in Compatible and Incompatible Defence Pathways
Article Snippet: .. The sequences were assembled using CAP3 software (default parameters except overlap length cutoff = 40 and overlap identity cutoff = 95) [ ], and in combination with some manual annotations, a unigene set of approximately 12 500 sequences was identified. .. Plasmids of the unigene set members were used as template for PCR amplification of the inserts using universal M13 primers.

Article Title: De novo transcriptomic analysis and development of EST-SSRs for Sorbus pohuashanensis (Hance) Hedl.
Article Snippet: .. The primary unigenes were assembled using CAP3 EST software to produce a final unigene set of 96,213 unigenes with an average length of 700 bp and N50 value of 894. .. The final unigene set contained 19,614 sequences (20.39%), with lengths less than 400 bp; 32,971 unigenes (34.27%), with lengths ranging from 401 to 600 bp; 14,962 unigenes (15.55%), with lengths ranging from 601 to 800 bp;8,582 unigenes (8.91%), with lengths ranging from 801 to 1000 bp; and 20,084 unigenes (20.87%), with lengths above 1000 bp ( ).

Construct:

Article Title: Whole-transcriptome analysis of differentially expressed genes in the ray florets and disc florets of Chrysanthemum morifolium
Article Snippet: .. The intra-scaffold gaps were filled and a non-redundant unigene set was constructed from all three assembled datasets using CAP3 software [ ]. ..

Generated:

Article Title: Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome.
Article Snippet: The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus.. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant.. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins.

other:

Article Title: Transcriptome Analysis of Syringa oblata Lindl. Inflorescence Identifies Genes Associated with Pigment Biosynthesis and Scent Metabolism.
Article Snippet: The primary unigene was further assembled to the final unigene with the CAP3 EST software[31].



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