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sh-miR / designer

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.
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Programy do SIRNA #3

Closed Nozdi closed 10 years ago

Nozdi commented 11 years ago

Projektowanie SIRNA, opensource ktory mozna postawic albo darmowego

nhlfr commented 11 years ago

Nie jestem pewien, czy do końca o to chodziło, ale do przyjrzenia się https://github.com/kinobus/kinome-stack + http://www.labkey.com na którym podobno bazuje https://github.com/WillForan/siRNAmotif

ghost commented 11 years ago

nie znam tych programów. Warto będzie przejrzeć :)

On 19 April 2013 21:50, Michał Rostecki notifications@github.com wrote:

Nie jestem pewien, czy do końca o to chodziło, ale do przyjrzenia się https://github.com/kinobus/kinome-stack + http://www.labkey.com na którym podobno bazuje https://github.com/WillForan/siRNAmotif

Reply to this email directly or view it on GitHubhttps://github.com/Nozdi/shmir/issues/3#issuecomment-16681250 .

ghost commented 11 years ago

Rules for selecting siRNA targets on mRNA sequences:

Targets should be located 50-100 nt downstream of the start codon (ATG). Search for sequence motif AA(N19)TT or NA(N21), or NAR(N17)YNN, where N is any nucleotide, R is purine (A, G) and Y is pyrimidine (C, U). Target sequences should have a G+C content between 35-60%. Avoid stretches of 4 or more nucleotide repeats. Avoid 5'URT and 3'UTR, although siRNAs targeting UTRs have been shown to successfully induce gene silencing. Avoid sequences that share a certain degree of homology with other related or unrelated genes.

http://www.protocol-online.org/prot/Protocols/Rules-of-siRNA-design-for-RNA-interference--RNAi--3210.html

ghost commented 11 years ago

http://sourceforge.net/projects/sirnarules/?source=directory open source w javie http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557693/

do sprawdzenia czy działają:

siDirect: http://design.rnai.jp/

Whitehead Institute siRNA: http://jura.wi.mit.edu/bioc/siRNAext/

Wistar Bioinformatics Gene-specific siRNA selector: http://bioinfo.wistar.upenn.edu/siRNA/siRNA.htm

Ambion siRNA design and databases: http://www.ambion.com/techlib/misc/siRNA_tools.html

Web RNAi databases

http://www.rnainterference.org/ http://nematoda.bio.nyu.edu/cgi-bin/rnai/index.cgi

rglsk commented 11 years ago

Odpaliłem http://design.rnai.jp/ , przeczytałem Helpa, wpisałem example human claudin i działało, wypisało jakieś rzeczy o których nie mam pojęcia, więc tak działa, ale czy o to nam chodzi - nie wiem ;)