I am trying to use EMBOSS water program to align several sequences stored in one fasta file to a sequence in another file. I'm NOT taking about multiple sequence alignment, I just want to align each sequence in the first file to the single sequence in the second file.
my first file looks like that:
>cel-let-7-3p MIMAT0015091 Caenorhabditis elegans let-7-3p CUAUGCAAUUUUCUACCUUACC >cel-lin-4-5p MIMAT0000002 Caenorhabditis elegans lin-4-5p UCCCUGAGACCUCAAGUGUGA >cel-lin-4-3p MIMAT0015092 Caenorhabditis elegans lin-4-3p ACACCUGGGCUCUCCGGGUACC
Water's documentation states that 'water reads a nucleotide or protein sequence and one or more sequence to be aligned to it. ' So I suppose what I want to do should be possible.
However, when I Insert the sequences to water, only the first sequence is aligned. I tried this with different sequences occupying the first position in the file so I know it's not because there are no alignments for the other sequences. Water just seems to ignore them.
I know this is possibly a stupid question, but I have no idea how to solve this and would appreciate your help
Thanks in advance