I have a long sequences file and another small sequences. I want to do an alignment (multiple or global) of small sequences on long sequences.
Do you suggest me the right software? of course I have two files, I do not know if we can make an alignment by taking two fihciers entered into.
thanks for your answers
> but the alignment tools do not accept two input file.
Adding more sequences to an already existing multi sequence alignment is often called 'profile aligning'. 'mafft' has three options for this purpose (--add, --addfragments, --addfull). Please read the mafft manual http://mafft.cbrc.jp/alignment/software/addsequences.html
here is my problem:
I have a file A of sequences DNA and a file B of sequence DNA.
I want to do a multiple sequence alignment of each sequence in file A with all sequences of B.
The problem is I have two files and according to my research there are no multiple alignment tools that accepts two files.
can you help me
If the number of of long sequences in the file is not too large, then you can format it as FASTA (if it isn't already) and use it as the reference to align the file of short sequences with any of the short read aligners.