Robert Penchovsky:Bioinformatics

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You can choose from the bioinformatics applications below.

EBWS - Bioinformatics

RevComOligo

If you want to have your reverse complementary DNA sequence click here…
RandomOligoGenerator

If you want to have random DNA, RNA or peptide sequences click here…
Motif Searcher

If you want to search for motifs in any DNA, RNA or peptide sequences click here…
Restriction Mapping

If you want to search for restriction sites in DNA sequences click here…
Prokaryotic ORF Finder

If you want to search for Open Reading Frames (ORFs) in prokaryotic DNA sequences click here…
DNA/RNA Mutations

If you want to perform random DNA or RNA mutations at different rates click here…
DNA/RNA TM Calculator

If you want to calculate the melting temperature (TM) of DNA or RNA click here…
Guide RNA Generator

If you want to generate guide RNA sequences for CRISPR/Cas9 system click here…
PCR Annealing Temperature Calculator

If you want to calculate the annealing temperature for PCR reaction click here…

You can choose from the bioinformatics applications below.

ExBWS-Bioinformatics

DNA/RNA Translator

If you want to translate DNA or RNA sequence click here…
AminoCODE

If you want to change a protein sequence from one letter code to three letters and vice versa click here…
Virtual PCR

If you want to perform a PCR reaction click here…
HydropathyPlot-Proteins

If you want to perform a Hydropathy plot of an amino acid sequence click here…
Reverse Translator

If you want to perform a Reverse translation of a protein sequence click here…
Eukaryotic ORF finder

If you want to search for Open Reading Frames (ORFs) in Eukaryotic DNA sequences click here…

You can use the bioinformatics database below.

Riboswitch database

RSwitch database

To browse the RSwitch database of riboswitches as antibacterial drug targets click here…

You can apply for allosteric ribozyme design software below.

Ribozyme generators

Oligonucleotide-sensing ribozyme generators

Generators of fast oligonucleotide-sensing ribozyme with YES (GHOST-YES) or NOT (GHOST-NOT) Boolean logic function click here…
Oligonucleotide-sensing ribozyme generator

A generator of slow oligonucleotide-sensing ribozyme with YES Boolean logic function click here…
Inverse ribozyme generator

An inverse generator of slow oligonucleotide-sensing ribozyme with YES Boolean logic function click here…

You can choose from the applications below.

More Applications

Bioinformatics Websites

NCBI…; BLAST…; EBI…; PrimerBLAST…; UCSC…; Rfam…; PDB…; KEGG…; BioCYC…;
IP Address

If you want to find out your current IP address please click here…
Calculator

If you want to calculate anything please click here…
Calendar

If you want to see a calendar please click here…

PCR annealing TM Calculator:

Enter your Forward and Reverse primer sequence (from a 5-prime end to a 3-prime end) to compute the annealing temperature of the primers. Add more primers for calculating TM for multiplex reaction. The TM of the primers is calculated according to the unified nearest-neighbor thermodynamics at 37^oC. Please use sequences above 15bp in length.

Taq Polymerase; Phusion Polymerase; Q5 Polymerase

Forward primer: 5'- -3'

Reverse primer: 5'- -3'

For multiplex reaction add up to 6 extra primers from below

Add primer 5' to 3' :

5'- -3'

Add primer 5' to 3' :

5'- -3'

Add primer 5' to 3' :

5'- -3'

Add primer 5' to 3' :

5'- -3'

Add primer 5' to 3' :

5'- -3'

Add primer 5' to 3' :

5'- -3'

Oligo Concentration (pmole):

MgCl₂ Concentration (mM):
(Applicable only in Taq)

*TMs for Phusion and Q5 polymerases are based on the use of the Hi-fidelity (HiFi) buffers provided respectively

When you use this bioinformatics applet please cite this paper.

Created together with Dr. D. Kaloudas. For any comments or inquires you can email him...

Robert Penchovsky's Website

EBWS - Bioinformatics

RevComOligo

RandomOligoGenerator

Motif Searcher

Restriction Mapping

Prokaryotic ORF Finder

DNA/RNA Mutations

DNA/RNA TM Calculator

Guide RNA Generator

PCR Annealing Temperature Calculator

ExBWS-Bioinformatics

DNA/RNA Translator

AminoCODE

Virtual PCR

HydropathyPlot-Proteins

Reverse Translator

Eukaryotic ORF finder

Riboswitch database

RSwitch database

Ribozyme generators

Oligonucleotide-sensing ribozyme generators

Oligonucleotide-sensing ribozyme generator

Inverse ribozyme generator

More Applications

Bioinformatics Websites

IP Address

Calculator

Calendar

Oligo Concentration (pmole): MgCl2 Concentration (mM): (Applicable only in Taq)

(Applicable only in Taq)

*TMs for Phusion and Q5 polymerases are based on the use of the Hi-fidelity (HiFi) buffers provided respectively

Created together with Dr. D. Kaloudas. For any comments or inquires you can email him...

Oligo Concentration (pmole):

MgCl₂ Concentration (mM):
(Applicable only in Taq)