About
This Smith-Waterman alignment program was originally written for an introductory Bioinformatics class in the spring of 2006.
While the Smith-Waterman alogrithm is a rather inefficient method for aligning large data-sets; aligning two sequences in O(n²) time (assuming both sequences are length n), there are many potential uses outside the field of Bioinformatics. For these reasons I designed my code to accept not only Protein and DNA input, but standard text input.
Valid Input
Aligned strings can be of four types:
- DNA
- protein
- text split on word
- text split on character
DNA:
When the DNA option is chosen all non letter characters are removed from the inserted text. Because of ambiguous nucleotides the content of the string is not checked to ensure that it is DNA. White spaces and new lines are removed and the program checks for fasta headers. Be sure to set the match and miss-match values to the desired values. Unlike proteins, DNA and text do not use scoring matrices to score matches and miss-matches
Protein:
When the protein option is chosen the string is checked to ensure that all characters are valid amino acid abbreviation. As with DNA, fasta headers and non string characters are searched for and removed. Aligning proteins utilizes one of the two optional scoring matrices. If you would like to align your protein sequences without using a scoring matrix just designate the string as DNA.
Text, split on character:
When this option is chosen, all white spaces are removed and the string is split by letter. As with DNA you should adjust the match and miss-match parameters, along with gap open and gap extension values if desired.
Text, split on word:
When one chooses this option the text is processed as before, but is split into words, not individual characters. This method of handling text is well suited to picking out quotes common to news articles on similar topics
About text output:
Text output will appear on one line when viewed in a browser. To view the alignment just save the page as a text document then open with a text editor.
please direct questions and comments to:
wtclarkatindianadotedu