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 - -

 

Examples:

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

 

Output:

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.

Job Openings

Wissenschaftlicher Mitarbeiter (m/w/d) 

 

Latest News

 

Our paper "GatekeepR: an R shiny application for the identification of nodes with high dynamic impact in boolean networks" has been published online first in Bioinformatics.

 

Our paper "The Necessity of Interoperability to Uncover the Full Potential of Digital Health Devices" has been published in JMIR Medical Informatics.

 

"Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients" has been published in npj Precision Oncology.

 

Our paper "AMBAR-interactive alteration annotations for molecular tumor boards" has been published in Computer Methods and Programs in Biomedicine.

 

"A protocol for the use of cloud-based quantum computers for logical network analysis of biological systems" has been published in STAR Protocols.

 

Our paper "A systems biology approach to define mechanisms, phenotypes, and drivers in PanNETs with a personalized perspective" has been published in npj systems biology and applications.

 

"Supporting SURgery with GEriatric Co-Management and AI (SURGE-Ahead): A study protocol for the development of a digital geriatrician" has been published in PLoS One.

 

"Self-Assessment of Having COVID-19 With the Corona Check Mhealth App" has been published in IEEE Journal of Biomedical and Health Informatics.


Our first quantum computing paper "Leveraging quantum computing for dynamic analyses of logical networks in systems biology" has been published in Patterns.