#secondary structure

[poopeepeepah]

Finally finished this 12x12 print for my lab. A companion piece to a much smaller logo I finished ages ago. I had put off finishing this print (the first of such ambition and size for me) for so long for fear of messing something up or not executing my initial vision I began to lose sight of what my initial vision for the project was… as I carved it and made proofs, I realized I might have done a couple minor things differently, but overall I really enjoy the final product. Sound off in the comments with the RNA secondary structures you recognize in the lettering! Also if you can tell what chemical mechanism the word “lab” is (very roughly / poorly) schematizing, I’ll extract all the RNA from your body (once reduced to homogenized tissue lysate) FOR FREE!

[rnaframework]

RNA Framework v2.5.2 released

This release fixes some critical bugs, and introduces a new feature. Now, RF Fold automatically generates SVG graphical summaries for each predicted structure (reactivity data, Shannon entropy, base-pairing probabilities and MEA structure):

So now, you will have your figures ready for publication in a few minutes, without any effort. Hope you'll enjoy it!

Check it out on GitHub!

[rnaframework]

RNA Framework v2.5 released

After several months of hard work, the RNA Framework v2.5 is finally here. Several major changes have been introduced:

1. RF Fold now supports the windowed folding of large RNA molecules through an approach based on the original method described by Siegfried et al., 2014 (PMID: 25028896). For additional details please refer to the documentation.

2. Libraries underwent a substantial rewrite to introduce pseudoknots support. Pseudoknotted structure are supported both from CT and dotbracket (Vienna) files. To enable the support of complex pseudoknotted RNA topologies, an expanded dotbracket alphabet has been introduced, based on the same standard used in Stockholm files. Let's consider the following sample structure:

The topology of this structure is too complex to be described using the standard dotbracket notation. Through the use of an expanded alphabet, the RNA Framework can now represent the previous structure as follows:

.....(((((....[[[.....{{{...<<<....AAA..))))).....]]].....}}}>>>.....aaa..

3. Introduced the RF JackKnife utility to perform jackknifing (grid search) of optimal slope/intercept folding parameters. For additional details please refer to the documentation.

4. Much more...

Check it out on GitHub!

[nextgenintelligence]

RNA Structure Framework v1.0.0a is out!

We are proud to communicate that RNA Structure Framework has been completely rewritten, and that version 1.0.0alpha is available for download.

New features include: - Full multi-threads support - Added Rouskin et al., 2014 method for data normalization - Added ViennaRNA package 2.2.0 support for soft-constraints

Check it out at: http://rsf.hugef-research.org

[nextgenintelligence]

Our article published on Bioinformatics

Our article “RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data“ has been published on Bioinformatics.

Check it out: http://goo.gl/TWC7ah

RSF is available at: http://rsf.hugef-research.org

[ijaarinnspub]

Comparative studies of Indian and Malaysian Thaparocleidus siamensis using molecular marker Saroj Rajvanshi, Nirupama Agrawal

Key words: Thparocleidus, comparative study, motif identification, secondary structure.

Abstract

In the present communication the sequence of an exotic species of genus Thaparocleidus i.e T. siamensis (Lim, 1990) Lim, 1996 (collected in India) has been compared with that of Malaysian, on in silico basis using 28S rDNA. Since, both are morphologically more or less similar and effect of environment on T. siamensis cannot access structurally. Thus to evaluate the environmental effects on 28S rDNA region of T. siamensis, a comparative study has been done for Indian (obtained) and Malaysian (retrieved) T. siamensis using MEME Suite, MARNA and ExpaRNA (online softwares)). The results obtained showing a shift in genetic material because of climatic changes in India.

Read Full Article: Volume 4, Number 1, January 2014 – JBES

Published on: International Journal of Agronomy and Agricultural Research (IJAAR)

[nextgenintelligence]

Our article published on Genome Biology

Our article "Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome" has been published on Genome Biology.

Check it out: http://goo.gl/9rq9VF

[test-tings-blog]

BIOLOGICAL MOLECULE: Define the term secondary structure

The coiling or folding of the primary structure of a protein molecule (localised folding) due to the formation of hydrogen bonds as the protein is synthesised. The main forms are the α-helix and the β-pleated sheet