MSA - optimize prealigned sequences - limit number of introduced gaps
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24 months ago


I have set of nucleotide sequences (ca 50bp) with 4 bases in each that I know they are aligned. Now, I would like to align different portion of the sequences (a strech of 6 nts ca 15 bases upstream) in such way, that only 0-2 gaps may be inserted between the new portion and the know 4 bases (this is biological constrain).

I know that there are some MSA that allow you to specify the bases that you know are aligned, but I'm unaware if there is any MSA program, that allows you to specify the maximum number of gaps.. ?

Thanks for any input

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