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.
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