RNA StrAT : RNA Structure Analysis Toolkit

نویسندگان

  • Valentin Guignon
  • Cedric Chauve
  • Sylvie Hamel
چکیده

Summary: We present a web server dedicated to the comparison of RNA secondary structures. This server allows to compare pairs of RNA secondary structures and to search, for a given RNA secondary structure, RNA genes with similar structures in a large database of RNA structures. The comparison and search are performed using an edit distance algorithm that considers a wide range of edit operations. Availability: The website is freely available without registration at http://www­lbit.iro.umontreal.ca/rnastrat/ Contact: [email protected]

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Relation Between RNA Sequences, Structures, and Shapes via Variation Networks

Background: RNA plays key role in many aspects of biological processes and its tertiary structure is critical for its biological function. RNA secondary structure represents various significant portions of RNA tertiary structure. Since the biological function of RNA is concluded indirectly from its primary structure, it would be important to analyze the relations between the RNA sequences and t...

متن کامل

Identification of RNA-binding sites in artemin based on docking energy landscapes and molecular dynamics simulation

There are questions concerning the functions of artemin, an abundant stress protein found in Artemiaduring embryo development. It has been reported that artemin binds RNA at high temperatures in vitro, suggesting an RNA protective role. In this study, we investigated the possibility of the presence of RNA-bindingsites and their structural properties in artemin, using docking energy ...

متن کامل

A zero one programming model for RNA structures with arclength ≥ 4

In this paper, we consider RNA structures with arc-length 4 . First, we represent these structures as matrix models and zero-one linearprogramming problems. Then, we obtain an optimal solution for this problemusing an implicit enumeration method. The optimal solution corresponds toan RNA structure with the maximum number of hydrogen bonds.

متن کامل

In silico Analysis and Molecular Modeling of RNA Polymerase, Sigma S (RpoS) Protein in Pseudomonas aeruginosa PAO1

Background: Sigma factors are proteins that regulate transcription in bacteria. Sigma factors can be activated in response to different environmental conditions. The rpoS (RNA polymerase, sigma S) gene encodes sigma-38 (σ38, or RpoS), a 37.8 kDa protein in Pseudomonas aeruginosa (P. aeruginosa) strains. RpoS is a central regulator of the general stress response and operates in both retroa...

متن کامل

‌RNA secondary structure and qRT-PCR analyses pertained to expressed anti-CD25 CAR in NK-92 cell line

Background and Objectives: Tumor-infiltrating regulatory T (TI-Treg) cells perform the significant function in cancer immune escape. In this study, the third generation CAR construct was designed against human CD25 antigen, the significant cell surface biomarker of TI-Tregs. Methods: Initially, the construct of anti-CD25 CAR was designed. Using RNAfold web server, the RNA secondary structure wa...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 2007