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.
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.