This repo contains a rough version of this alignment algorithm written in Perl. Right now, all it provides is the grid, which can then be used for scoring the different sequences.
- The currrent version of this script can only align two DNA/protein sequences that are of equivalent length.
- It assumes a linear gap penalty of -1 using the PAM250 scoring matrix.
- Try it out!
Under the ShinyApp directory are the current versions of the shiny app that has been published at https://nmerwin.shinyapps.io/NW-Alignment.
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The currrent version of this script can only align two DNA/protein sequences.
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Only does the Needleman-Wunsch algorithm.
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Sequences are limited to the width of your screen.. it gets all wonky after that!
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Try it out, and give me feedback (post an issue on the repo)
Current plans for updates:
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Include drop down menu for Global / Local alignment
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Format printed aligned sequences (Kinda done.. could be much better)
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Work on JS processing for layout.
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Print out summary statistics for aligned sequences (ex. number of gaps, number of matches, total score??)
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Print out aligned sequences (remove matrices) -- DONE!!
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Drop down menu for scoring matrices (ex. Ts/Tv, PAM, BLOSUM, etc) --- DONE!!
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Allow for initation/extension gap penalties --- DONE!!