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DNA Melting - stitchprofiles.uio.no - Stitch Profile

DNA Melting - Stitch Profile. Choose a type of calculation. How to input a sequence. Upload a sequence file:. The sequence's GI number:. Insert DNA sequence (copy/paste):. Extract DNA sequence fragment (optional):. Default [begin-end] to get the full sequence. Default [begin-end] to get the full sequence. Maximum sequence length: 140000 bp. Stitch profile parameters input. How to handle stitch profile parameters. Choose a temperature: T =. Choose a helicity: θ =. Interval: [0.5 - 6].

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DNA Melting - Stitch Profile. Choose a type of calculation. How to input a sequence. Upload a sequence file:. The sequence's GI number:. Insert DNA sequence (copy/paste):. Extract DNA sequence fragment (optional):. Default [begin-end] to get the full sequence. Default [begin-end] to get the full sequence. Maximum sequence length: 140000 bp. Stitch profile parameters input. How to handle stitch profile parameters. Choose a temperature: T =. Choose a helicity: θ =. Interval: [0.5 - 6].

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DNA Melting - stitchprofiles.uio.no - Stitch Profile | stitchprofiles.uio.no Reviews

https://stitchprofiles.uio.no

DNA Melting - Stitch Profile. Choose a type of calculation. How to input a sequence. Upload a sequence file:. The sequence's GI number:. Insert DNA sequence (copy/paste):. Extract DNA sequence fragment (optional):. Default [begin-end] to get the full sequence. Default [begin-end] to get the full sequence. Maximum sequence length: 140000 bp. Stitch profile parameters input. How to handle stitch profile parameters. Choose a temperature: T =. Choose a helicity: θ =. Interval: [0.5 - 6].

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DNA Melting - stitchprofiles.uio.no - About

http://stitchprofiles.uio.no/about.php

DNA Melting - About. Welcome to stitchprofiles.uio.no. This server performs web-based computations on DNA melting, thus predicting the localized separation of the two strands for sequences provided by the users. The primary tool here is the stitch profile. A diagram representing the alternative conformations that partly melted DNA can adopt. This new type of diagram is an alternative to the ordinary probability profiles for describing the conformations and their statistics at a given temperature. And the...

2

DNA Melting - stitchprofiles.uio.no - Loop Entropy

http://stitchprofiles.uio.no/loopentropy.php

DNA Melting - Loop Entropy. Choose a type of calculation. This page contains an online tool for calculating the parameters of a Fixman-Freire loop approximation for arbitrary DNA sequence length and loop exponent given as user input. The exact loop entropy factor is. Is the loop size (one plus the number of melted basepairs), σ is the cooperativity (or nucleation or initiation) constant,. Where the power function is replaced by some multi-exponential function. Are determined by fitting. In the range [2:2.

3

DNA Melting - stitchprofiles.uio.no - Glossary

http://stitchprofiles.uio.no/glossary.php

DNA Melting - Glossary. I) that the basepair at sequence position i is closed (i.e. helix). This term has been used in the DNA melting litterature to denote both probability profiles and temperature profiles. A differentiated melting curve, i.e. -dθ/dT as a function of T. For intermediate length sequences (10. Also called the mean degree of helicity. The average of all the basepairing probabilities, θ =(p. A plot of the helicity as a function of temperature. For intermediate length sequences (10. The tem...

4

DNA Melting - stitchprofiles.uio.no - Help page

http://stitchprofiles.uio.no/help.php

DNA Melting - Help page. Stitch profile parameters input. How to specify a temperature range for a melting curve. How to specify one or more probability profiles. How to choose a probability level for a temperature profile. This help page contains usage instructions and documentation. Helpful explanations of melting concepts can also be found in the glossary. For general info about this website, conditions of use and litterature references, see the about. Upload a sequence file. 241 caacttgtta tttttgccga...

5

DNA Melting - stitchprofiles.uio.no - Temperature Profile

http://stitchprofiles.uio.no/ctemp_prof.php

DNA Melting - Temperature Profile. Choose a type of calculation. How to input a sequence. Upload a sequence file:. The sequence's GI number:. Insert DNA sequence (copy/paste):. Extract DNA sequence fragment (optional):. Default [begin-end] to get the full sequence. Default [begin-end] to get the full sequence. Sequence length limitation: 20000bp. Choose probability level for the temperature profile. How to handle the temperature profile. Choose Loop Entropy Factor:. Exact power law (slow).

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Only in current section. Prediction of beta-barrel outer-membrane proteins. Collection of web-based tools particularly useful for genome-wide analyses. A generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets. Interactive analysis of consolidated protein interaction data and their supporting evidence from iRefIndex. Calculation of ratio of nonsynonymous (Ka) to synonymous (Ks) nucleotide substitution rates. Graphical ...

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Conferences and training courses. The Oslo part of the FUGE Bioinformatics platform. We are gradually building up services. Presently, we can point you to the following:. A microarray database and analysis tools. This site offers services within phylogenomic and database searches. Sequence searching, a part of the Salmon Genome Project. A database specifically designed to store protein 3D model structures. A part of the Salmon Genome Project. Communal site for Norwegian SNP allele frequency information.

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DNA Melting - stitchprofiles.uio.no - Stitch Profile

DNA Melting - Stitch Profile. Choose a type of calculation. How to input a sequence. Upload a sequence file:. The sequence's GI number:. Insert DNA sequence (copy/paste):. Extract DNA sequence fragment (optional):. Default [begin-end] to get the full sequence. Default [begin-end] to get the full sequence. Maximum sequence length: 140000 bp. Stitch profile parameters input. How to handle stitch profile parameters. Choose a temperature: T =. Choose a helicity: θ =. Interval: [0.5 - 6].

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