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)
2017
PMCID: 5729218
PMID: 29242834
DOI: 10.1128/mSphere.00488-17

[…] 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 […]

2014
PMCID: 4014442
PMID: 24810276
DOI: 10.1371/journal.pgen.1004281

[…] 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 […]

2013
PMCID: 3833222
PMID: 24136150
DOI: 10.1038/bjc.2013.637

[…] 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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