User: glarue

gravatar for glarue
glarue20
Reputation:
20
Status:
New User
Location:
United States
Website:
https://github.com/glarue
Last seen:
4 months, 1 week ago
Joined:
4 years ago
Email:
e***********@gmail.com

Posts by glarue

<prev • 11 results • page 1 of 2 • next >
0
votes
2
answers
317
views
2
answers
Answer: A: very high maximum-likelihood dS values from PAML
... I posted [a similar question][1] to the PAML Google Group and received a response from the author: > this is a common problem and also commonly discussed. basically your > sequences are too divergent, and synonymous changes are saturated. > below i have copied a paragraph from my book. z ...
written 4 months ago by glarue20
0
votes
2
answers
317
views
2
answers
very high maximum-likelihood dS values from PAML
... I have a set of putative paralogous transcript pairs (identified via reciprocal BLASTing) that I've aligned at the protein level and backtranslated. I would like to calculate dS for each pair. I have run the alignments through PAML (nucleotide), but am getting very high (>60) dS values for many ...
dn/ds alignment paml written 12 months ago by glarue20
0
votes
1
answer
812
views
1
answers
Comment: C: what is the problem with using clustal to do pairwise alignment?
... Thanks for the response. What I'm after, though, is a better understanding of *why* EMBOSS recommends against using Clustal for pairwise alignments - presumably they're worse than those produced by, say, NEEDLE, but in what way? What sort of issues might I see in the alignments that would be amelior ...
written 12 months ago by glarue20
0
votes
1
answer
812
views
1
answers
Comment: C: what is the problem with using clustal to do pairwise alignment?
... Good point - no, they were both set to use the default values. I can't figure out how to set the gap penalties for Clustal Omega, but using ClustalW I tried setting the values to be the same as NEEDLE and this resulted in yet another, different, alignment. ...
written 12 months ago by glarue20
0
votes
1
answer
812
views
1
answers
Comment: C: what is the problem with using clustal to do pairwise alignment?
... So, I ran a comparison between Clustal Omega and NEEDLE (EMBOSS's recommended pairwise alignment tool) and, disconcertingly, with default options they both definitely give different alignments: ![different alignments][1] By eye, I guess the Clustal ones do seem worse but I'm not confident in my abi ...
written 12 months ago by glarue20
1
vote
1
answer
812
views
1
answer
what is the problem with using clustal to do pairwise alignment?
... I have a set of putatively-paralogous protein sequence pairs that I'm trying to align. I (naively) used Clustal Omega to generate pairwise alignments, but am getting some weird downstream results (abnormally high dS values between many pairs) so I went back through the documentation and noticed that ...
alignment written 12 months ago by glarue20 • updated 12 months ago by Hussain Ather890
0
votes
1
answer
1.7k
views
1
answers
Answer: A: Getting genbank annotation file from JGI
... AFAIK, JGI does not provide data in GenBank format, so you will have to use a tool to convert the FASTA + GFF3 combo to GenBank. Here is a discussion of one such tool from EMBOSS. If you're going to be pulling multiple datasets from JGI and you'd like to use the command line, you may find useful a ...
written 3.2 years ago by glarue20
2
votes
1
answer
2.2k
views
1
answers
Answer: A: How To Retrieve Data From Jgi Automatically Given A Set Of Ids?
... I know this is a late response, and it may not do exactly what you need, but feel free to check out a script I wrote to do something similar here: https://github.com/glarue/jgi-query   It's written in Python and runs from the command line. I haven't tested it on Mac or Windows, but it should (theo ...
written 3.4 years ago by glarue20
0
votes
1
answer
3.0k
views
1
answers
Comment: C: fastq-dump stream to named pipe (fifo) to Trinity
... Thanks for this. It got me on (what I think will be) the right track. ...
written 4.0 years ago by glarue20
0
votes
1
answer
3.0k
views
1
answers
Comment: C: fastq-dump stream to named pipe (fifo) to Trinity
... Thanks for the response! I am unsure of the advantage of --split-spot over --split-files, but you've outlined the general strategy I've decided on. I've messed around a bit with some simple awk regex parsing of the convolved --split-files -I -Z output, where the -I flag should allow me to separate t ...
written 4.0 years ago by glarue20

Latest awards to glarue

Popular Question 3.1 years ago, created a question with more than 1,000 views. For fastq-dump stream to named pipe (fifo) to Trinity

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1020 users visited in the last hour