by Ivano Zara with the help and advice of Riccardo Schiavon
Comments and observations are welcome. Please, write to ivano.zara.bio @ gmail.com
In this section, have been grouped, the software used to build the primers
using the Nearest-Neighbor thermodynamic parameters

  • Human Genomic PickPrimer
    (create PCR Primers on regions without variants reported in various DBs)
     
  • Sequence PickPrimer
    (pick primers from a DNA sequence)
     

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 (New Release 2024_04)
    (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)

  • Primer Sequencing Analysis
    (Analysis of primers used for Sanger sequencing)
     
  • ABI Chromatogram
    (online ABI sequence Chromatogram)
     
  • Chromatogram Align
    (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
    • Rev/Comp any sequence
      (Reverse And Complemetary any sequence)
       
    • Join Sequence in IUPAC format
      (combines multiple nucleotide sequences into one in IUPAC format)
       
    • IUPAC code Table

       
  • Mix PCR
    (helps to mix the components of a PCR reaction)
     
  • Melting Profile
    (Oligo Melting Temperature Statistic)
     

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


  • determines the chromosomal position from one genomic release to another (from hg19 to hg38 and vice versa and now hs1 too)
     
  • Human Genomics Sequence (hg19/hg38)(with variants)
    (returns the sequence of a human genomic region with colored polymorphisms as a function of frequency)
     

  • Aligns mRNA sequences (with variants) with genomic and protein from genomic o mRNA position
     
  • 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 testing) "); (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