Primer catalog/databasing - (Oct/16/2012 )
Ok, so I have been having trouble remembering where all my primers are located. I have all their sequences in a little spreadsheet, but I can never remember where along my gene/gene area they are located. I try searching for their sequences in DNAstar seqbuilder, but that won't find the primer sequence if there is any nucleotide differences at all. But I am working with different clones/species of potato, so the specific sequence along the gene isn't always the same. So when I need to go back a few months to use some older primers, I can never figure out exactly where they prime.
Sometimes I can use a BLAST alignment to find the spot, but often I cannot.
Does anyone know of any programs, or services that would allow me to input a long sequence of genomic DNA, then match my primers to it, allowing for some ambiguity in the search? Then perhaps log all my primers into a catalog or something of the sort, so it would be easy to find them when I need them?
/also, if this is not in the correct place, please move it, or tell me where it should go.
I wanted to catalogue all our primers once, but found mostly a paid programs (though one had a trial and wasn't that bad, but I can tell you the name when I'll return to work).
Actually so far better than spreadsheet is just have the sequences (the whole primer3 output actually) in plaintext files. But better light-weight text editor is needed to work with these, like Notepad2 or Notepad+ (freeware).
Search within text file is quick, you can search contents of text files even globally.
When I need to keep the sequence and the primer position I use Word. If you copy there long genomic sequence without word wrap, Word can search though line ends. (BUT in Word joining lines is painfully complicated, so if you copy a FASTA sequence from NCBI to the Notepad2 first, then select Join lines, then find the invisible character appearing inbetween the joined lines and Replace it with nothing, you get contininuous sequence in no time, then copy this to Word)
You can then use the highlight tool to highlight the position of your primers on that sequence. Or use hyperlink. Or bookmark. Or whatever there is.
You can have multiple variants of sequences in one file, and then search for different version of primers using exact sequence (you would need online/macro reverse transcription tool for rew primers). But one think I don't really understand, how you want to search primers that don't exactly match? I don't think any tool except for Blast or Align2seq can do that. And if that doesn't help (doesn't align the not-so matching primers) then I'm affraid nothing can.
I've seen some complex sequence-manipulating suites (like Vector NTI), that could search through double stranded sequence (not sure about the incomplete alignment) but most of them were pretty heavy duty for task you can do with text file and Word, and what's important they are all paid.