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by Ivano Zara with the help and advice of Riccardo Schiavon
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DNA hybridization reaction
If you are interested in understanding, examining in detail the DNA hybridization reaction, understanding the melting temperature, what it is and how to arrive at its final equation, also, being able to calculate the fraction of hybridized ss strand as a function of temperature and arriving at its final equation by developing in detail all the easy mathematical steps.
Then here you are in the right place, click on the link DNA hybridization reaction
New app and relase 2025
In this section, have been grouped, the software used to build the primers
using the Nearest-Neighbor thermodynamic parameters


  • (create PCR Primers on regions without variants reported in various DBs)
     

  • (pick primers from a DNA sequence)
     
This section contains the software that analyze PCR products (amplicons)
and the software that analyze the oligonucleotide sequences and the primers sequences

  • (Analysis Template and Primer secondary structure in PCR reaction)
     

  • (Melting temperature and Thermodynamic Details of DNA Hybridization)
     

  • (hairpin-loop, dimer, bases penality and melting temperature)
     

  • (Analysis of primers used for Sanger sequencing)
     

  • (Analyze formations of structures (dimers and hairpin-loops) between different primers used in multiplex reactions)
     
In this section are grouped the software related
to the sequencing with the Sanger methods
(analysis of primers and chromatograms)


  • (Analysis of primers used for Sanger sequencing)
     

  • (online ABI sequence Chromatogram)
     

  • (Align multiple chromatograms with a polymorphic reference sequence)
     

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

  • Sequence utility

    • (Reverse And Complemetary any sequence)
       

    • (combines multiple nucleotide sequences into one in IUPAC format)
       


    •  
  • Mix PCR
    (helps to mix the components of a PCR reaction)
     

  • (Oligo Melting Temperature Statistic)
     
This section contains applications related to the human genome and mRNA

  • determines the chromosomal position from one genomic release to another (hg19, hg38 and hs1 )
     

  • (returns the sequence of a human genomic region with colored polymorphisms as a function of frequency)
     


  • shows the position of the exons and the coding sequence
     


  • Aligns mRNA sequences (with variants) with genomic (cDNA) and protein
    New: link with HGVS_easy
     
This section contains applications for analyzing genomic variants


  • (utility to easily write variants in HGVS format and pre-normalize them)


  • Shows details of a human variant such as the biological effect, isoforms, any related diseases and Pubmed citations.
    Converts the descriptions of the human variants (genomics, mRNA and protein) in the forms HGVS, VCF and local.

     

  • Appliation for analyze HLA alleles sequence
     
  • PriorVar (under construction)
    Management of genomic variants from human exome sequencing
    (Prioritization of genomic variants, contained in a VCF file, using functional consequence,
    customizable pathogenicity rancking score and LSDB Disease (currently only ClinVar))
     
    • 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