OTHER SITES

CLEANER (cellbiol.com) Offers and useful alternative by stripping off nonsequence material (e.g. numbers) from nucleic acid and protein sequence.  N.B. Particularly useful if you only want part of the DNA sequence from GenBank. Other sites offering a program to convert sequence format are Readseq (D.G. Gilbert, Univ. Indiana, U.S.A.) and fmtseq: A BioSeq File Format Converter.
Nucleic Acid Sequence Massager  (Allotron Biosensor Corporation) - my favourite which in addition to removing spurious material (numbers, breaks, HTML, spaces) changes the format (upper to low case, complement, reverse, RNA to DNA, and triplets). 
DNA Sequence Reverse and Complement (cellbiol.com) - With this tool you can reverse a DNA sequence, complement a DNA sequence or reverse and complement a DNA sequence. It also removes numbers, spaces, tabs, slash or non-GATC characters; and,  allows conversion to upper or low case.

For a bit of fun visit their site Secret Coder Tool to encode secret messages in DNA sequence.

Radioactive decay: see Radioactive Decay Calculator  (1728 Software Systems) or Radioactive Decay Calculator 2 .

  Centrifuge Helper (D.Wang, Oklahoma State University, U.S.A.) provides one with maximum RPM, RCF (ave, min, max), K factor and comparison between two rotors (Sorvall, Beckman, Composite, Eppendorf, IEC and Piramoon) or Centrifuge Rotor Speed Calculator (Science Gateway) .

Calculations (Zbio.net, Russia) Spectrophotometric measurement of nucleic acids concentration; Conversion: speed of rotation [krpm] - Relative Centrifuge Force [kg];  


Conversion: radioactivity - biological amount of dNTP's;
Conversion: weight - moles (for proteins).
Conversion: weight - moles (for nucleic acids).
Conversion: DNA - protein.
Conversion: molar quantity - molar concentration.
Conversion: units of measurement. 
Estimation of  time for bacteria growth.

Protocols (Zbio.net, Russia) - provides an incredible set of data and calculators for:

Densities of liquids
Densities of salt solutions
Densities of acids, alkali and organic compounds
Salt solutions (part one)
Salt solutions (part two)
 

BioMath Calculators (Promega Corp., U.S.A.) - DNA and protein unit conversions; temperature (C, F  & K); and, Tm calculations for oligonucleotides, includes adjustments for Mg+2 concentration. Highly recommended.

Nucleic acid calculator(Kenkyuu-Ryuugaku NET) or Oligo Calc: Oligonucleotide Properties Calculator -   From A260nm calculate DNA, RNA and oligonucleotide concentrations online.
Physical mapping calculator - library construction (Andrei Grigoriev) shows diagrammatically how the clone size and number influence what percentage of the genome is covered.

Biological buffer calculator (R. Beynon, Dept. Veterinary Preclinical Sciences Univ. Liverpool, England) - controls for concentration, ionic strength and temperature. For pKa data see here (Sigma-Aldrich).
Phosphate Buffer Calculation (Jeffrey Clymer) - A Java applet that calculates the amount of monosodium phosphate and trisodium phosphate necessary to achieve a buffer with a given pH and strength. 

Dilution Calculator (www.restrictionmapper.org/) - this very useful site for the mathematically challenged provides percent by weight, weight per volume and molarity of solution from stock solutions or solids.

Sites which permit one to carry out a variety of analyses include:

EMBOSS (European Molecular Biology Open Source  Software Suite) - can be accessed here (Open Bio Foundation, U.S.A.).  A list of their programs is appended.  The java version of these programs (JEMBOSS) can be accessed here (Agricultural Biotechnology Center, Hungarian EMBnet Node) and here (Stothard Research Group, University of Alberta, Canada)

SeWeR (SEquence analysis using WEb Resources) (The Bioinformatics Organization, MBIdeas Innovation Center, U.S.A.) - is also a java suite for analyzing nucleic acids and proteins.
The Biology WorkBench (San Diego Supercomputing Center, Univ. California San Diego, U.S.A.).
Sequence Manipulation Suite or here (Bioinformatics Org).
ProSAL (Structural Biology Labs, Biomedical Centre, Uppsala, Sweden) - an excellent Meta site for protein analysis and characterization.
Structure Prediction Meta-server (Bioinformatics Laboratory, BioInfoBank Institute, Poland) - runs PDB-Blast, ORFeus, FFAS, 3D-PSSM, GenTHREADER, mGenTHREADER, INBGU, ShotGun-INBGU, Sam-T99, FUGUE2, SUPERFAMILY, Jpred2, and PsiPred.

PAT: a protein analysis toolkit for integrated biocomputing on the web - (Reference: J. Gracy & L. Chiche. 2005. Nucl. Acids Res. 33: W65-71). Help is here.

 SCRATCH Protein Predictor (Institute for Genomics and Bioinformatics, University of California, Irvine, USA) - includes ACCpro: Solvent Accessibility;  ACCpro20: Solvent Accessibility (20 Class; SSpro: Secondary Structure (3 Class; SSpro8: Secondary Structure (8 Class); DISpro: Disorder; CONpro: Contact Number; CMAPpro: Contact Map; SVMcon: New SVM Contact Map; 3Dpro: Tertiary Structure; DOMpro: Domains;  DIpro: Disulfide Bonds; SOLpro: Solubility upon Overexpression; and, COBEpro: Continuous B-cell Epitopes

 

Updated: October 28, 2012