merger joins two overlapping nucleic acid sequences into one merged sequence.

Here is a sample session with merger:

% merger
Merge two overlapping nucleic acid sequences
Input sequence: tembl:eclacy
Second sequence: tembl:eclaca
Output sequence [eclacy.fasta]:
Output alignment [eclacy.out2]:

Typically, one of the sequences will need to be reverse-complemented to put it into the correct orientation to make it join. For example:

% merger file1.seq file2.seq -sreverse2 -outseq merged.seq -outfile stdout

Mandatory qualifiers:

[-seqa] (sequence)

Sequence USA.

[-seqb] (sequence)

Sequence USA.

[-outseq] (seqout)

Output sequence USA.

[-outfile] (align)

Output alignment and explanation.

Optional qualifiers:

-datafile (matrixf)

This is the scoring matrix file used when comparing sequences. By default, it is the file EBLOSUM62 (for proteins), or the file EDNAFULL (for nucleic sequences). These files are found in the data directory of the EMBOSS installation.

-gapopen (float)

Gap opening penalty.

-gapextend (float)

Gap extension penalty.