In-Silico PCR protocols
In-Silico PCR specifications
Information
| Unique identifier | OMICS_02344 |
|---|---|
| Name | In-Silico PCR |
| Interface | Web user interface |
| Restrictions to use | None |
| Output data | A file containing all sequence in the database that lie between and include the primer pair. |
| Output format | FASTA |
| Computer skills | Basic |
| Stability | Stable |
| Maintained | Yes |
Documentation
Maintainers
- person_outline UCSC Genome Informatics Group <>
- person_outline Jim Kent <>
In-Silico PCR IN pipelines
(3)[…] rrna loci, which make these regions suitable to resolve fungi to the species level (41). the newly combined silva-unite database, termed sis (18s-its1-5.8s), made it possible to then perform in silico pcr testing since the forward and reverse primer targets were present on each contig. the sis database contains 5,789 simulated reference sequence contigs representing 3,842 fungal […]
Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8
[…] primer pairs were designed from coding-exon sequences (cds) using primer3 [100] (opt. amplicon 200 bp, primer 18–25 bp, opt. tm 60°c, max. δtm 1°c, min. gc clamp 2 bp, max. homopolymer 3 bp). in silico pcr screening via e-pcr [101] required ≤1 amplicon (10 bp to 10 kbp) versus genome assembly and cds sequences. quantitative pcr was performed with 2 technical replicates and 3 biological […]
[…] using primer3 (http://frodo.wi.mit.edu/) to flank exons (supplementary materials). the sequences were then filtered using oligocalc software (kibbe, 2007) to avoid hairpin formation and ucsc in silico pcr software to ensure yield of a single product. dna from any ffpe sample in which a mutation was found was extracted twice independently and the pcr was repeated at least twice […]
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