User: mnsp088

gravatar for mnsp088
mnsp08840
Reputation:
40
Status:
New User
Location:
Last seen:
1 month ago
Joined:
6 months, 1 week ago
Email:
m*******@hotmail.com

Posts by mnsp088

<prev • 20 results • page 1 of 2 • next >
0
votes
1
answer
114
views
1
answers
Comment: C: Genome duplication assessment
... Thank you for your helpful suggestion, I will try this method out. ...
written 10 weeks ago by mnsp08840
0
votes
1
answer
161
views
1
answers
Comment: C: Extract Identical hits from pairwise global alignments
... That makes sense. thank you again! ...
written 11 weeks ago by mnsp08840
0
votes
1
answer
161
views
1
answers
Comment: C: Extract Identical hits from pairwise global alignments
... https://www.biostars.org/u/20598/ Just a side question out of curiosity - can one use blastp to do this task? I know it is used for local alignments but can we modify the command line arguments to make it perform a global alignment? ...
written 11 weeks ago by mnsp08840
0
votes
1
answer
161
views
1
answers
Comment: C: Extract Identical hits from pairwise global alignments
... This method worked perfectly. thank you for your thorough explanation and example code! ...
written 11 weeks ago by mnsp08840
4
votes
1
answer
161
views
1
answer
Extract Identical hits from pairwise global alignments
... Hi! I am trying to perform 1:1 pairwise global alignments for a bunch of proteins in a fasta file. My end goal is to get a total number of identical hits (I.e. proteins which have a perfect match from start to end). So far I am using this code from Biopython to perform those alignments: fasta ...
alignment protein biopython written 11 weeks ago by mnsp08840 • updated 11 weeks ago by Joe15k
0
votes
0
answers
88
views
0
answers
Comment: C: Improving assembly via normalizing reads
... Thank you, Mensur. I will give this + Blobtools a shot! ...
written 4 months ago by mnsp08840
0
votes
0
answers
88
views
0
answers
Comment: C: Improving assembly via normalizing reads
... Thank you for you suggestions and the linked paper. I will attempt binning to remove bacterial contigs. It seems there are many different methods of binning ([here][1]) Do you suggest any particular method to start with for this particular problem? [1]: https://en.m.wikipedia.org/wiki/Binning_(m ...
written 4 months ago by mnsp08840
0
votes
1
answer
125
views
1
answers
Comment: C: Clustering method for p-value data
... Thanks https://www.biostars.org/u/56237/ ! I tried converting to -log10 and re-running, now all Y's are in the same cluster (regardless of -I inflation value) as you suspected. ...
written 5 months ago by mnsp08840
0
votes
1
answer
125
views
1
answers
Comment: C: Clustering method for p-value data
... Thank you for the explanation, I think that makes sense, can you just elaborate further on why the edges of X1 to Y1-Y3 are zeros? I think I need to look into 1D discretization/segmentation instead for this problem.. ...
written 5 months ago by mnsp08840
0
votes
1
answer
125
views
1
answers
Comment: C: Clustering method for p-value data
... Thank you, basically the purpose is to assign the most representative Y for X1. I do not want to go with the smallest p-value because there are others such as Y2 and Y3 which are also extremely small and significant, so I am trying to group the Y's in some meaningful automated way. For example somet ...
written 5 months ago by mnsp08840

Latest awards to mnsp088

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1604 users visited in the last hour