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TOOLS AND LINKS

SCRIPTS

Java Script based page you can download and use in your PC. The script will help you to calculate the Melting Temperature of a primer, Micrograms of Double-Stranded DNA
to picomoles, Picomoles of Double-Stranded DNA to micrograms and nanograms, Micrograms per milliliter of oligonucleotides (Single-Stranded DNA) to picomoles per microliter etc.
 
Java Script will assist you in selectin of PCR primers. Something Similar writan in VB script for MS Word download here  
Calculation of Proten Concentration

MS Excel template with VB script for calculation of the unknown Protein concentration based on known standards fitted to a strait line using Linear Least Square method. Very simple but efficient for Bradford or other calorimetric assays. download here

 

TOOLS

Clustal is by far the best freeware for alingment of DNA and protin sequences. This is espesially true for multi sequence alingment. You can used on line or download PC, MAC or Linax version Align
Blast align Align two DNA/Protein sequences with BLAST align. Align

Pedros Tools

 

The biggest collection of Proteomics and Molecular Biology tools I am aware of.

Combo
DNAsis Max Hitachi DNASIS is set of tools for DNA and Proteins. Working DEMO is available. I don't know haw is the new demo, but I like the old one. It is awesome, maybe because I am use to it ..... Combo
Oligo Explorer 1.2(beta)

Good tool to design PCR primers similar to OLIGO. Works under Windows and it is free...

 
OLIGO6

This is the best PCR primer design software. Unfortunately, it is not free. DEMO is available but it is crippled, and no cracks are possible. There are other options for freeware and online primer selection, but it is not worth even mention them.

PCR
Vector NT Another Software Combo from Invitrogen , many tools mainly for cloning and primer selection. DEMO is available, you can find cracks for some old versions. Combo
pDRAW32 Really cool Freeware for PC only, Everyone has to have it. It is free it is equal or even better then Vector NT Combo

Other Tools

WEB Cuter2 & NEB cuter

These on line tools are similar and create DNA restrictian map. Very fast and good when you digest large DNA sequences.

 

Enzyme digest
Repeat Masker Since sequencing centers had compleated several genom progects and have established up-to-date libraries repetitive DNA masking DNA tools are available. It is a good idea for any genomic DNA manipulations to use one of this tools before hend and avoid suprising results. And here one interesting fact acording to the author on average, almost 50% of a human genomic DNA sequence currently will be masked .

DNA Masker

NOC Download NOC Structure
COOT Download COOT Structure
VISTA VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.  
UCSC Genome Bioinformatics Site This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides a portal to the ENCODE project.  
Genomatix DNA tools ____Log: dfarkas Pass: Dia7as999  
GENEART AG Order your own synthetic gene  

Protocols

Download local protocols Protein Engineering protocols-basic lab protocols-download pdf file.  
Download local protocols Plant molecular biology related protocols - download pdf file.  
Protocol Online Big colection of protocols on-line  
More on Line protocos There some good protocos here...  

Molecular Biology Protocols

Check somo PCR related protocols