DnaPromix Menu

Create Primer
Analysis Oligo & Primer
Analysis PCR Product
Sequencing
Tools
Human Genomics

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)

Note:
If you use programs to create primers (for PCR or sequencing), we remind you that on this platform there are
special apps currently used by some universities and scientific sites.
shows some scientific sites that have linked to use the primer programs

Technische Universitaet Carolo-Wilhelmina zu Braunschweig, DE
RWTH Aachen University, DE
Universitatsspital Zurich, CH
Universitaet Basel, CH
Mayo Foundation Medical Education and Research, US
Istituto Zooprofilattico Sperimentale della Sardegna
Universita' degli Studi di Padova
Universita' degli Studi di Padova (Treviso)
Universita' degli Studi di Padova, IT, Legnaro
Universita' degli Studi di Roma Tor Vergata
Universita' degli Studi di Modena e Reggio Emilia
Universita' degli Studi di Salerno
Ajou University, KR,
United Institute of Informatics Problems of National Academy of Sciences of Belarus
Szeged University Association, HU
CNR Torino, IT, Turin
Vienna University Computer Center, AT
Haidian, AS4538 China Education and Research Network Center

Furthermore, if you work with 'human' sequences, there are apps (Human Genomic PickPrimer)
that controls or avoids the construction of primers in polymorphic regions (sNPs etc.)

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 ...

- Human Genomic Position Converter (old and new version)
  - Old version (hg19/hg38)
  - New version (hg19/hg38/hs1)
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)

- Human Align Transcript (with variants)
  - from transcript position
  - from genomic position
Aligns mRNA sequences (with variants) with genomic and protein from genomic o mRNA position
- Human DNA Variant card
  from genomic or mRNA,
  (also convert HGVS and VCF format)
  - from Genomic data
  - from mRNA data (in hgvs format)
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.

- HLA (Human Leukocyte Antigens)
  - HLA windowAlign and Browser loci in short sequence
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))