PAGE 9: Useful links

In this page are reported some useful links

CGSG - E.coli genetic stock center

http://cgsc2.biology.yale.edu/

Huge  collection of  non-pathogenic strains of Escherichia coli: (predominantly K-12 derivatives). It includes cultures of wild-type contributed from a number of laboratories and thousand derivatives carrying from one or up to 29 mutations from among 3500 mutations in more than 1300 different loci.  

Costs: 

Fee for academic or no-profit companies:  $10 per each strain plus $35 distribution fee for each order placed.

Fee for profit companies:  $130/strain. For 5+ strains the fee is reduced to $120/strain. For 15+ strains the fee is reduced to $110/strain

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ADDGENE - The no-profit plasmid repository

http://www.addgene.org/

Collection of over 70,000 plasmids contributed by 4,100 research labs around the world
Costs:
Fee for academic or no-profit companies: 
$65 per each plasmid plus up to single $45 distribution fee for each order placed. Reduced fee for >6 plasmids
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Centrifuge SPEED calculators

Beckman calculator
Eppendorf-centrifuge-speed-calculator
Thermofisher rpm vs rcf-calculator

to readily convert RPM on RCF(g) or vice-versa
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IMGT
http://www.imgt.org/vquest/refseqh.html

access to sequences in FASTA format is constituted by sets of immunoglobulin (IG) or T cell receptor (TR)  which are isolated from the IMGT reference sequences
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Basic Bio-informatic Tools

DNA sequence analysis:

Calculate the primer properties:  Oligocalculator 

DNA  reverse complement sequence

Restriction enzime finder: WebCutter; NEBCutter

Protein sequence analysis

Secondary structure prediction -  Secondary Consensus PBIL
Signal peptide prediction - SignalP server
LPXTG motif  prediction - CW Pred
Conserved domain finder - SMART
Sequence alignment - ClustalW PBIL

Topology Prediction: DAS, TMHMM, CCTOP

Prediction of N- C- O- Glicosilation in mammalian: N-GLyc, O-GLyc - C-GLyc)

Therapeutic antibodies pre-developability profiler (in silico) - TAP 
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Image J Download (nih.gov)

 is a Java-based image processing program developed at the National Institutes of Health free available for download. 

ImageJ can calculate area and pixel value statistics of user-defined selections and intensity-thresholded objects. It can measure distances and angles. It can create density histograms and line profile plots.

It can be used to perform several routine operation in laboratory as densitometric protein quantification from SDS-page or automatic cell count 

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Chromas

(download at  http://technelysium.com.au/wp/chromas/) 

a free simple, easy-to-use sequence viewer and editor 

(able to open chromatogram files(.ab1) produced from automated Sanger sequencers)

 that could be used to check your sequencing results.

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DicroProt  (https://dicroprot-prabi.ibcp.fr/)

a simple tool designed to integrate into a single package most of the methods designed for the estimation of protein sequence secondary structure derivation from circular dichroism experiments. I used it extenivelly during my PhD several years ago and it works quite well in my opinion.
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