User: trinityduke100

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Posts by trinityduke100

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Finding suboptimal alignments
... No worries. Thank you very much and apologies for repeatedly asking the same thing. ...
written 1 day ago by trinityduke10010
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Comment: C: Finding suboptimal alignments
... I completely understand you but I am testing a mathematical model of a noisy channel. For which I need the probability of the suboptimal alignments occurring. Is there any other (efficient) way to find the suboptimal alignments? One method that was suggested was to use forward backward algorithm, ...
written 2 days ago by trinityduke10010
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Comment: C: Finding suboptimal alignments
... But given that there are exponentially large number of possible alignments, isn't there any efficient alternative? ...
written 3 days ago by trinityduke10010
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Comment: C: Finding suboptimal alignments
... But what I understand is that Smith-Waterman algorithm is for local alignment and not for global alignment? ...
written 3 days ago by trinityduke10010
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Finding suboptimal alignments
... I have been trying to find an efficient way to find the suboptimal alignments given two sequences. I understand that we can use Needleman-Wunsch algorithm to find optimal alignments but what about suboptimal alignments? Is there a way to find suboptimal alignments? Could we use forward algorit ...
sequencing alignment dna written 3 days ago by trinityduke10010 • updated 3 days ago by Mensur Dlakic9.0k
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Equivalent of Waterman-Eggert Algorithm
... I am trying to figure out ways to find suboptimal alignments for sequences. I know that Needleman - Wunsch gives the optimal alignment. I also know that Waterman-Eggerton algorithm is a modification of the Smith-Waterman algorithm which gives suboptimal sequence alignments. However, how do you ...
sequencing alignment dna written 27 days ago by trinityduke10010
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Comment: C: Getting alignments with lower scores on Biopython
... Is there a way to find alignments of lower scores apart from the method I mentioned above which also gives the probability of each assignment? Or is the modified Needleman - Wunsch the only way? ...
written 5 weeks ago by trinityduke10010
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Pairwise2 Gap penalty function for insertion errors
... I am trying to compare 2 sequences sequence A and Sequence B. Seq A is the original loss-less equation and equation B is the sequence with errors. I am using Biopython (pairwise2) to solve my problem. def gap_function(x, y): # x is gap position in seq, y is gap length if y == ...
python alignment biopython sequencing written 5 weeks ago by trinityduke10010
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Comment: C: Getting alignments with lower scores on Biopython
... So do you mean that all(or most) alignments which have a lower score are meaning-less(say we fix the length of the sequence)? Lets say even if its less by 1 point? I understand what you are saying but I am not 100% convinced. ...
written 5 weeks ago by trinityduke10010
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Comment: C: Pairwise2 Alignment Gap Penalties
... Yes but is this for substitutions(mismatch) errors? I have a particular sequence that is passed through a channel which results in insertion, deletion and substitution errors. I have these probabilities but all insertions and deletions appear as gaps in the alignments. ...
written 5 weeks ago by trinityduke10010

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