Team:AMU-Poznan/Project
From 2014.igem.org
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sh-miR Designer is a software aimed for fast and efficient design of effective RNA interference (RNAi) reagents - sh-miRs, also known as artificial miRNAs. sh-miRs are RNA particles whose structure is based on miRNA precursor pri-miRNA, but sequence interacting with transcript is changed depending on research purpose. Maintenance of structure of pri-miRNA is very important to enable cellular processing and therefore ensure functionality of artificial particles. sh-miRs delivered to cells on genetic vectors - plasmids or viral vectors - enter natural RNAi pathway and silence target mRNA. They can be used in genetic therapies and basic biomedical research. | sh-miR Designer is a software aimed for fast and efficient design of effective RNA interference (RNAi) reagents - sh-miRs, also known as artificial miRNAs. sh-miRs are RNA particles whose structure is based on miRNA precursor pri-miRNA, but sequence interacting with transcript is changed depending on research purpose. Maintenance of structure of pri-miRNA is very important to enable cellular processing and therefore ensure functionality of artificial particles. sh-miRs delivered to cells on genetic vectors - plasmids or viral vectors - enter natural RNAi pathway and silence target mRNA. They can be used in genetic therapies and basic biomedical research. | ||
We will provide two applications to access the software, one which require siRNA sequences and the second which require transcript accession number from NCBI database. Each user will receive an account with login (e-mail) and password where he/she would be able to check history of software usage. | We will provide two applications to access the software, one which require siRNA sequences and the second which require transcript accession number from NCBI database. Each user will receive an account with login (e-mail) and password where he/she would be able to check history of software usage. | ||
- | <br/> | + | <br/>input form:<br/> |
<img src="https://static.igem.org/mediawiki/2014/2/24/Zrzut_ekranu_2014-10-15_o_18.07.36.png" width="60%"></br> | <img src="https://static.igem.org/mediawiki/2014/2/24/Zrzut_ekranu_2014-10-15_o_18.07.36.png" width="60%"></br> | ||
+ | users' history:<br/> | ||
+ | <img src="https://static.igem.org/mediawiki/2014/c/c2/Zrzut_ekranu_2014-10-15_o_18.09.10.png" width="60%"><br/> | ||
+ | |||
<h1>Standard Parts</h1> | <h1>Standard Parts</h1> | ||
</br> | </br> | ||
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<img src="https://static.igem.org/mediawiki/2014/b/bb/Shmir-STANDARD.png" width="60%"></br> | <img src="https://static.igem.org/mediawiki/2014/b/bb/Shmir-STANDARD.png" width="60%"></br> | ||
<h1>User Guide</h1> | <h1>User Guide</h1> | ||
- | </br></br> | + | <h3>Usage via Web server</h1> |
+ | go to our website <a href="shmir.wmi.amu.edu.pl">shmir.wmi.amu.edu.pl</a> | ||
+ | <h3>Usage via client</h3> | ||
+ | </br>Fold sequence via mfold:</br> | ||
+ | |||
+ | ./shmir_client.py mfold ACTGAUUUGAC</br> | ||
+ | Create sh-miR from one siRNA strand (active) or two siRNa strands separated by space.</br> | ||
+ | First strand is active, both are in 5-3 orientation</br></br> | ||
+ | |||
+ | ./shmir_client.py from_sirna UUUGUAUUCGCCCUAGCGC CGCUAUGGCGAAUACAAACA</br> | ||
+ | Create sh-miR from transcript name.</br> | ||
+ | Optional parameters</br> | ||
+ | |||
+ | --min_gc : Minimal "GC" content in strand -- default: 40</br> | ||
+ | --max_gc : Maximal "GC" content in strand -- default: 60</br> | ||
+ | --max_offtarget : Maximal offtarget in strand -- default: 10</br> | ||
+ | --mirna_name : The name of miRNA backbone to use -- default: "all"</br> | ||
+ | --stymulators : One of ["yes", "no", "no_difference"] -- default: "no_difference"</br> | ||
+ | ./shmir_client.py from_transcript NM_001618.3 --mirna_name miR-30a --min_gc 22</br> | ||
<h1>Technology</h1> | <h1>Technology</h1> | ||
</br>The application was built with Python 2.7. It is divided into 3 parts:</br> | </br>The application was built with Python 2.7. It is divided into 3 parts:</br> |
Revision as of 16:26, 15 October 2014
sh-miR Designer v2.0Sh-miR designer is a project we started during iGEM 2013. This year we would like to continue and expand functionality of the software. sh-miR designer v1.0 (link) is aimed to create sh-miR molecules based on siRNAs provided by the user. In sh-miR designer v2.0 only the mRNA number (from NCBI database), which expression should be decreased can be provided. Moreover, we expanded functionality of the software with off-target validation and check of immune motifs and also extended miRNA-shuttles database. sh-miR Designer is a software aimed for fast and efficient design of effective RNA interference (RNAi) reagents - sh-miRs, also known as artificial miRNAs. sh-miRs are RNA particles whose structure is based on miRNA precursor pri-miRNA, but sequence interacting with transcript is changed depending on research purpose. Maintenance of structure of pri-miRNA is very important to enable cellular processing and therefore ensure functionality of artificial particles. sh-miRs delivered to cells on genetic vectors - plasmids or viral vectors - enter natural RNAi pathway and silence target mRNA. They can be used in genetic therapies and basic biomedical research. We will provide two applications to access the software, one which require siRNA sequences and the second which require transcript accession number from NCBI database. Each user will receive an account with login (e-mail) and password where he/she would be able to check history of software usage.input form: users' history: Standard PartsWe are creating a particle which can be inserted into plasmid built by Standard parts from Registry of Standard Biological Parts.User GuideUsage via Web server
go to our website shmir.wmi.amu.edu.pl
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