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So, here are two links I use frequently:
Primer3: a web interface for designing primers for an imput sequence. This link puts you at the source code page. Just click 'user interface' and you're ready to roll
http://frodo.wi.mit.edu/primer3/primer3_code.html
Ensembl: a database for genetic/genomic architecture. I use it to find promoter/enhancer sequences for designing primers and amplicons (with Primer3) for ChIP and also to find exon/intron splice sites so that my amplicons for Real-Time PCR span a splice site such that only cDNA and not genomic DNA is amplified.
http://www.ensembl.org/
WI SiRNA design program: a web interface like Primer3 for designing RNA hairpins to silence RNA expression. Run by the Whitehead Institute of MIT, a user inputs a mRNA sequence and the program gives specific short hairpins to knockdown gene expression. You need to make a username and password, but it's free and worth it.
http://jura.wi.mit.edu/pubint/http://iona.wi.mit.edu/siRNAext/home.php
Primer3: a web interface for designing primers for an imput sequence. This link puts you at the source code page. Just click 'user interface' and you're ready to roll
http://frodo.wi.mit.edu/primer3/primer3_code.html
Ensembl: a database for genetic/genomic architecture. I use it to find promoter/enhancer sequences for designing primers and amplicons (with Primer3) for ChIP and also to find exon/intron splice sites so that my amplicons for Real-Time PCR span a splice site such that only cDNA and not genomic DNA is amplified.
http://www.ensembl.org/
WI SiRNA design program: a web interface like Primer3 for designing RNA hairpins to silence RNA expression. Run by the Whitehead Institute of MIT, a user inputs a mRNA sequence and the program gives specific short hairpins to knockdown gene expression. You need to make a username and password, but it's free and worth it.
http://jura.wi.mit.edu/pubint/http://iona.wi.mit.edu/siRNAext/home.php