by Ivano Zara with the help and advice of Riccardo Schiavon
February 2020, new application: PriorVar (Management of human genomic variants from human exome sequencing) (in the 'Human Variants' tab)
In this section, have been grouped, the software used to build the primers
using the Nearest-Neighbor thermodynamic parameters

In this section the software that analyze the oligonucleotide sequences
and in general the primers used in the PCR reaction have been grouped

  • Oligo Melting
    (Melting temperature and Thermodynamic Details of DNA Hybridization)
     
  • PCR Primer Analysis
    (hairpin-loop, dimer, bases penality and melting temperature)
     
  • Sequencing Primer Analysis
    (Analysis of primers used for Sanger sequencing)
     
  • Primer Multiplex PCR
    (Analyze formations of structures (dimers and hairpin-loops) between different primers used in multiplex reactions)
     

This section contains the software that analyze or search for PCR products (amplicons)


  • Amplicon Analysis
    (Analysis Template and Primer secondary structure in PCR reaction)
     
  • ThermoHybrid PCR (UNDER CONSTRUCTION)
    (In silico PCR with amplicon analysis (for bacteria fingerprint and other) )
     
  • Blast PCR (UNDER CONSTRUCTION)
    (I....) )
     
In this section are grouped the software related
to the sequencing with the Sanger methods
(analysis of primers and chromatograms)


In this section there are various tools that help manipulate nucleotide sequences or create PCR reactions

This section contains the software to analyze human genomic variants ...


Some of these applications are / were also installed at Promix: CRIBI (University of Padua)
Sorry, but the CRIBI server is out of order at the moment

2019-12 Last internal database updates with files, tables or App:
- Genomic versions GRCh37/hg19 and GRCh38/hg38 available
- HGNC (Custom Download) for gene names and synonyms.
- RefGene from UCSC: To loacalize the exonic boundaries of transcripts in genomic sequences
- RefMrna from UCSC: for transcripts sequences.
- LRG_RefSeqGene from NCBI: to match the IDs of the transcripts (NM_ *) to the IDs of the proteins (NP_ *) 
     and the standard transcripts of the genes
- refLink from UCSC: as above
- App Eutils from NCBI: as above.
- dbSNPs 151 for SNPs variants from NCBI.
- For allelic frequencies: GnomAD v2.1.1 for GRCh37/hg19 (exomes and genomes), v3.0 for GRCh38/hg38 (genomes).
Note: If the standard transcripts could not be obtained with LRG_RefSeqGene, 
      then the longest transcript of the gene was used