I recommend watching my explanation video before watching this: ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-bQ7kRW6zo9Y.html @Theblackin Pearls noticed that there was an error in the code. It's fixed now in the code link in Github and it's not a major change (compare the code in the video with code currently on Github!). The error is in the function find_solution as I was calling OPT[:m][:n] like this as if it were a matrix but it's not as it's a list of lists which doesn't work the same as matrices. Instead just call it with the entire OPT and it should work fine.
good video,but still has two little issue .1.I spent half hour ,try to understand why the recurisive function need to return OPT[:][:], and then , I find it doesn't matter.....you just need to return OPT 2. in the recurisive function (selection) insert has a higher priority than others (align, delect)
hello! cool vid and nice explanation. I want to ask if it works for long sequences like those of length 10000 for example because it is giving me list index out of range for such long sequences
Yeah you were right that there was an error in the code. In find_solution I was indexing in OPT as if it were a matrix (but it's a list of lists) causing indexing to be incorrect. Instead of doing OPT[:m][:n] which changes the OPT "matrix" incorrectly, instead just call the function with OPT. I pinned a comment that there's an error in the code displayed in the video. An updated code on Github is linked in the comment in the video, it's a minor change but makes a big difference. Thanks for commenting and noting this mistake
hat is the average score of the global alignment between 2 random DNA sequences of length 3? Use the following scoring scheme: a match is +1, mismatch is -1 and both opening and extension gap penalty is -0.5. Show your steps
Irving Rondon @Alladin Persson, So far python codes videos for the implementation of the Smith-Waterman Algorithm, Scoring Matrices, General gap Penalty, Dot Matrices will be very useful
Thanks for your comment, it was a while since I did this but if I get some spare time I'll try to look into this, are these different algorithms or variants of Sequence Alignment?
@@AladdinPersson this is used for sequence alignment (dna rna and protein) golbalxx is used for dna and mrna while globalds and other are used mainly for proteins. I got this explanation from various books but not quite sure.
