You hereby assure to have read and agree to our cookies and GDPR Disclaimer (Datenschutzerklärung). More info and Privacy policy. Got it!

Medical Systems Biology

You are here:  Software > Swat > 2. Running Swat

2. Running Swat

change into the directory, where you unpacked swat and use the following command line to run swat:

java -jar swat.jar protein.fasta nucleotide.fasta

Important: The files of the protein sequence and the nucleotide sequence have to be in fasta-format and must end with ".fasta". The protein sequence has to be followed by the nucleotide sequence.


Parameters and defaults:

 to control the alignment, the following parameters can be set. If not explicitly specified, the default will be used.


Parameter Meaning Range Default
g= penalty for starting a gap -10000 to -1 -10
e= penalty for extending a gap -10000 to -1 -1
s= penalty for a single frameshift -10000 to -1 -20
d= penalty for a double frameshift -10000 to -1 -40
p= penalty for a stop codon mismatch -10000 to -1 -4
m= scoring matrix (path to matrix-file) - BLOSUM62
ng no gaps are allowed in the alignment true / false false
na no affine gap scoring is used true / false false
nf no frame shift mutations are allowed true / false false
w use the worst case calculation for wild bases true / false false
o= define a file to save the found mutations in a file in json format - -



java -jar swat.jar prot.fasta nucl.fasta g=-12 e=-2 s=-15 d=-30 m=matrices\PAM250 w

= align prot.fasta and nucl.fasta with a gap open penalty of 12 and gap extend penalty of 2. framshifts are scored with -15 and -30. As scoring matrix the PAM250 matrix is used in the folder "matrices". Also a worst case calculation is used for the wild bases.

java -jar swat.jar prot.fasta nucl.fasta ng nf o=mutas.json

= perform an alignment without gaps or frameshifts and save the mutations in the file mutas.json



the commandline output contains the identifier of the aligned sequences, the length of the squences, a list of the used parameters, the alignment score (Smith-Waterman score), the start and the end positions of the local alignment and the length of the alignment.

Also a detailed alignment is displayed.

swat alignment protocol

Explanation of the Markers in the detailed output:

||| = exact match of an amino acid and a nucleotide triplet
+++  = positive match of an amino acid and a nucleotide triplet
***  = mismatch / replacement of an amino acid and a nucleotide triplet
III  = insertion of a codon in the nucleotide sequence
DDD  = deletion of a codon in the nucleotide sequence
|-x  = frameshift deletion at position x
-xy  = doubleframeshift deletion at position x and y
||i  = frameshift insertion at position 3 of a codon
|i|  = frameshift insertion at position 2 of a codon
i||  = frameshift insertion at position 1 of a codon
|ii  = frameshift insertion at position 2 and 3 of a codon
i|i  = frameshift insertion at position 1 and 3 of a codon
ii|  = frameshift insertion at position 1 and 2 of a codon

 Finally informations about the amount of identical matches, positve matches, gaps, mutations and wild bases is displayed.

Latest News


Our paper "Unraveling the Molecular Tumor-Promoting Regulation of Cofilin-1 in Pancreatic Cancer" has been published in MDPI Cancers.


Our paper "Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases" has been published online first in Briefings in Bioinformatics.