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.
|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.
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.
Our first quantum computing paper "Leveraging quantum computing for dynamic analyses of logical networks in systems biology" has been published in Patterns.
Our paper "Unsupervised domain adaptation for the detection of cardiomegaly in cross-domain chest X-ray images" has been published in Frontiers in Artificial Intelligence.
"Vaccine Side Effects in Health Care Workers after Vaccination against SARS-CoV-2: Data from TüSeRe:exact Study" has been published in Viruses-Basel.
"PREDICT-juvenile-stroke: PRospective evaluation of a prediction score determining individual clinical outcome three months after ischemic stroke in young adults – a study protocol" has been published in BMC Neurology.
Our paper "Federated Electronic Data Capture (fEDC): Architecture and Prototype" has been accepted for publiaction in the Journal of Biomedical Informatics.
Our paper "Efficient cross-valdation traversals in feature subset selection" has been published in Scientific Reports.
Our paper "CANTATA - prediction of missing links in Boolean networks using genetic programming" has been published in Bioinformatics.
Our paper "Interaction Empowerment in Mobile Health: Concepts, Challenges, and Perspectives" has been published in the Journal of Medical Internet Research mhealth and uhealth.
Our paper "Identification of dynamic driver sets controlling phenotypical landscapes" has been published in the Computational and Structural Biotechnology Journal.
Congratulations to Dr. Silke Werle for winning the 1st Prize with her pitch at the 1. Science Day held by ProTrainU.
Our paper "Reconstructing Boolean network ensembles from single-cell data for unraveling dynamics in the aging of human hematopoietic stem cells" has been published in the Computational and Structural Biotechnology Journal.
The position paper "Is there a role for statistics in artificial intelligence" has been published online first in Advances in Data Analysis and Classification.