Dear all
I'm trying to aling short sequences composed by units of 3 characters. I use 3 characters because I need to codify at least 6000 different entities (enzymes in this case). An example of this kind of sequences could be: ABC ADC ADX ... ( I put an space after each 3 letters, in fact this sequence is ABCADCADX).
Probably exist any software that allow to choose the number of characters that in fact be an unique unit of alignment. Also I need to introduce a my own similarity matrix (different that the usual like Blosum62)
Please, do you know any software that could help?
Thank you in advance
Benjamí
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benjap700 •
You can use EMBOSS needle (for global) or water (local) alignment. They allow a custom substitution matrix as input using the -datafile option. You can use the command:
embossdata -fetch -file EDNAFULL
to copy the DNA default matrix to your working directory and change it to use only three letters by setting the scores to a very low number. See more here: http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/water.html
Thank you, Asaf All the best :)
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benjap700 •
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Am I understanding this right that you're trying to do codon-aware alignment?
If not, you might need to explain further, perhaps showing some ideal output.
Thank you for your quick answer, Joe
No, I'm not trying to align codons, but the problem is similar: I need to codify my units of alignment with 3 characters, because I have to codify 6000 entities (enzymes in this case). Then, my sequences are composed by units of 3 letters and the software must consider this fact.