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.). See also CONVERT
Sequence cleanup or formatting - offers: 60 characters per line, UPPER CASE, lower case, GenBank, and skyline
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.
Good Calculators: Free Online Calculators - This website provides a variety of online calculators, math and physics, engineering and conversion calculators.
Nucleic acid calculator(Kenkyuu-Ryuugaku NET) or Oligo Calc: Oligonucleotide Properties Calculator - From A260nm calculate DNA, RNA and oligonucleotide
Physical mapping calculator - library construction(Andrei Grigoriev) - shows diagrammatically how the clone size and number influence what percentage of the genome
Biological buffer calculator (R. Beynon, Dept. Veterinary Preclinical Sciences Univ. Liverpool, England) - controls for concentration, ionic strength and temperature.
Also available here. For pKa data see here (Sigma-Aldrich). Other buffer sites include: Science Gateway Buffer Calculator, and Buffer Calculator
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 (SourceForge, U.S.A.). A list of their programs is appended. Some of threse tools can be accessed at the EMBL-EBI site. The java version of these programs (JEMBOSS) can be accessed here.
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.). No longer funded.
Sequence Manipulation Suite or here (Bioinformatics Org).
ProSAL (Structural Biology Labs, Biomedical Centre, Uppsala, Sweden) - an excellent Meta site for protein analysis and characterization.
GeneSilico Meta-server (Bioinformatics Laboratory, BioInfoBank Institute, Poland) - (Reference: Kozlowski LP & Bujnicki JM. 2012. BMC Bioinformatics 13: 111). this is a gateway to various methods for protein structure prediction. If you submit a single protein sequence or a multiple sequence alignment (hereafter called a "target"), you should obtain the following predictions: (a) Primary structure: domains identified by HmmPfam and HHSearchCDD; (b) Secondary structure: helical/extended/other conformation (H/E/-) sspro4, cdm, psipred, fdm, jnet, prof, gor, spine, sable, pssfinder, sspred, sspal, nnssp, ssp, NetSurfP, SOPRANO, (c) Transmembrane helices: Phobius, MEMSAT3, TMpred, HMMTOP, DAS, MINNOU, OCTOPUS, TMHMM2.0, (d) Disordered regions: DisEMBL,RONN, IUPRED, POODLE-L, GLOBPLOT, DISPROT(VSL2), PrDOS, DISOPRED2, Spritz, disPRO, Pdisorder, Spritz, iPDA, POODLE-S (calculated consensus is CASP8 winning method in the category); (e) Disulfide bonds: DiANNA, DISULFIND, DBCP and DIpro2.0, (f) Nucleic acid binding residues in proteins: BindN, BindN+, DISIS, DP-Bind, PPRInt, and our meta-predictor for RNA-binding residues (cons3best) and (g) Tertiary structure
PAT: a protein analysis toolkit for integrated biocomputing on the web - (Reference: J. Gracy & L. Chiche. 2005. Nucl. Acids Res. 33: W65-71).
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.
PSIPRED Protein Sequence Analysis Workbench - includes PSIPRED v3.3 (Predict Secondary Structure); DISOPRED3 & DISOPRED2 (Disorder Prediction); pGenTHREADER (Profile Based Fold Recognition); MEMSAT3 & MEMSAT-SVM (Membrane Helix Prediction); BioSerf v2.0 (Automated Homology Modelling); DomPred (Protein Domain Prediction); FFPred 3 (Eukaryotic Function Prediction); GenTHREADER (Rapid Fold Recognition); MEMPACK (SVM Prediction of TM Topology and Helix Packing) pDomTHREADER (Fold Domain Recognition); and, DomSerf v2.0 (Automated Domain Modelling by Homology). (Reference: Buchan DWA et al. 2013. Nucl. Acids Res. 41 (W1): W340-W348).
MESSA: Meta-Server for protein sequence analysis - provides secondary structure (PSIPRED, SSPRO); coil and loop (DISEMBL) and flexible loop (DISEMBL) analysis, identification of low complexity (SEG) and disordered regions (IsUnstruct, DISOPRED, DISEMBL,DISPRO); transmembrane helices (TMHMM, TOPPRED,HMMTOP, MEMSAT); TM Helices and signal peptides (MEMSAT_SVM, Phobius); signal peptides (SignalP HMM Mode, SignalP NN Mode); coiled coils (COILS) and positional conservation. Multiple Sequence Alignment of confident BLAST hits, filtered by less than 90% identity and more than 40% coverage, are used to calculate the positional conservation indices of residues in the sequence. The conserved residues usually play important roles in maintaining the function or structure of a protein. The residues are highlighted from white, through yellow to dark red as the conservation level increases. Function Prediction: This section contains predicted function annotation, GO terms and EC numbers (if the query is an enzyme). A confidence level ("very confident", "confident" or "probable") is provided for each prediction. (Reference: Q. Cong & N.V. Grishin. BMC Biology 2012, 10:82).
Rtools (Computational Biology Research Consortium , Japan) - is a bioinformatics web Server for RNA (single FASTA format, <= 400nt) - In order to visualize the whole picture of the distribution of the secondary structure, this web-server provides users with rich information of single RNA sequences using 7 tools: (a) CentroidFold based on a generalized centroid estimator is one of the most accurate tools for predicting RNA secondary structures. (b) CentroidHomfold predicts RNA secondary structures by employing automatically collected homologous sequences of the target. (c) IPknot predicts RNA secondary structures including a wide class of pseudoknots. (d) Rchange computes entropy and internal energy changes of secondary structures for single-point mutated sequences. (e) CapR calculates probabilities that each RNA base position is located within each secondary structural context for long RNA sequences. (f) Raccess computes the accessibility of segment [a, b] = [x, x+l-1] in the transcript for all the positions x with fixed length l (Acc.len) = 5, 10, 20. (g) RintD validates RNA secondary structures. Target secondary structures are predicted by CentroidFold (inference engine: McCaskill) and RNAfold (Minimum free energy structure).