## User: trinityduke100

trinityduke100 •

**10**- Reputation:
**10**- Status:
- New User
- Location:
- Last seen:
- 1 day, 9 hours ago
- Joined:
- 1 month, 1 week ago
- Email:
- t*************@gmail.com

#### Posts by trinityduke100

<prev
• 14 results •
page 1 of 2 •
next >

0

votes

1

answer

61

views

1

answers

Comment:
C: Finding suboptimal alignments

... No worries. Thank you very much and apologies for repeatedly asking the same thing.
...

written 1 day ago by
trinityduke100 •

**10**0

votes

1

answer

61

views

1

answers

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
trinityduke100 •

**10**0

votes

1

answer

61

views

1

answers

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
trinityduke100 •

**10**0

votes

1

answer

61

views

1

answers

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
trinityduke100 •

**10**0

votes

1

answer

61

views

1

answer

... 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 ...

written 3 days ago by
trinityduke100 •

**10**• updated 3 days ago by Mensur Dlakic •**9.0k**0

votes

0

answers

92

views

0

answers

... 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 ...

written 27 days ago by
trinityduke100 •

**10**0

votes

2

answers

280

views

2

answers

... 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
trinityduke100 •

**10**0

votes

0

answers

84

views

0

answers

... 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 == ...

written 5 weeks ago by
trinityduke100 •

**10**0

votes

2

answers

280

views

2

answers

... 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
trinityduke100 •

**10**0

votes

1

answer

172

views

1

answers

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
trinityduke100 •

**10**#### Latest awards to trinityduke100

No awards yet. Soon to come :-)

Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.

Powered by Biostar
version 2.3.0

Traffic: 1684 users visited in the last hour