User: shpak.max

gravatar for shpak.max
shpak.max0
Reputation:
0
Status:
New User
Last seen:
1 month ago
Joined:
5 years, 11 months ago
Email:
s********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by shpak.max

<prev • 7 results • page 1 of 1 • next >
0
votes
0
answers
93
views
0
answers
Input arguments to list ancestral sequences in emboss phylip (dnapars)
... I need to generate a phylip outfile with the inferred ancestral DNA sequences at each node of a tree. Phylip provides this option, and the default setting returns a reference sequence (reconstructed at the ancestral node) and subsequent sequences denoted by "." if there is no change and by a nucleot ...
phylip emboss written 6 weeks ago by shpak.max0 • updated 7 days ago by Biostar ♦♦ 20
0
votes
1
answer
145
views
1
answers
Comment: C: EMBOSS program for calculating dN/dS from MSA
... Thanks. The protocols.io site is temporarily down, so I have a quick question: when PAML computes dn/ds, does it take a tree file as input along with the MSA (and thus count the actual number of substitutions based on tree nodes), or does it do pairwise comparisons of all sequences regardless of phy ...
written 8 weeks ago by shpak.max0
1
vote
1
answer
145
views
1
answer
EMBOSS program for calculating dN/dS from MSA
... Does EMBOSS have an associated program that will calculate dN, dS (non-synonymous/synonymous substitutions) for a multiple sequence alignment? If so, what is the program, and can it use a tree file to determine the actual number of substitutions rather than just tallying the raw number based on pai ...
emboss written 8 weeks ago by shpak.max0 • updated 8 weeks ago by Mark800
0
votes
1
answer
92
views
1
answer
Creating .phy files in clustal without truncation
... I have a set of sequence files with very long names. If I use clustal-omega for MSA, the .fasta format output retains the full sequence name. However, if I create an MSA in .phy (PHYLIP) format, the sequence name is automatically truncated to 10 characters. I tried to get around this by first creat ...
clustal phylip written 11 weeks ago by shpak.max0 • updated 11 weeks ago by Mensur Dlakic6.5k
0
votes
1
answer
1.3k
views
1
answers
Comment: C: DAVID and Panther can't identify certain Uniprot Accessions
... What, if any, options do I have for running these accessions through the standard annotation tools? ...
written 3.4 years ago by shpak.max0
2
votes
1
answer
1.3k
views
1
answer
DAVID and Panther can't identify certain Uniprot Accessions
... I obtained a list of differentially expressed proteins from MS/MS data, and have been trying to use gene annotation tools like DAVID and Panther to get functional enrichment information, pathways, etc. I've noticed that DAVID etc. are able to obtain data for Uniprot accessions that begin with P or ...
panther gene annotation david uniprot written 3.4 years ago by shpak.max0 • updated 3.4 years ago by Elisabeth Gasteiger1.7k
0
votes
0
answers
2.1k
views
0
answers
minimum information content in .maf to run mutsig
... I have been filtering and annotating vcf's generated by SomaticSniper and MuTect, and would like to run my mutation calls through MutSig to identify which genes have significant numbers of non-synonymous mutations. I think that the simplest way for me to do so is to take my data and construct a .maf ...
mutsig written 5.9 years ago by shpak.max0 • updated 6 weeks ago by Biostar ♦♦ 20

Latest awards to shpak.max

Popular Question 3.0 years ago, created a question with more than 1,000 views. For minimum information content in .maf to run mutsig
Popular Question 5.9 years ago, created a question with more than 1,000 views. For minimum information content in .maf to run mutsig

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1134 users visited in the last hour