User: jnf3769

gravatar for jnf3769
jnf376940
Reputation:
40
Status:
New User
Location:
United States
Last seen:
1 week, 2 days ago
Joined:
2 years, 2 months ago
Email:
j******@g.rit.edu

Posts by jnf3769

<prev • 17 results • page 1 of 2 • next >
0
votes
0
answers
99
views
0
answers
Comment: C: Alignment as BLAST-able database/other alignment avenues
... While I thank you for your response, you again are missing the spirit of the question. The gaps are necessary. It would not be an alignment if I removed the gaps, nor would it inform me to the delineations of the protein sequences in the alignment. ...
written 10 days ago by jnf376940
0
votes
0
answers
99
views
0
answers
Comment: C: Alignment as BLAST-able database/other alignment avenues
... Well, that is what I consider the old fashioned way. But in any case, you've completely missed the spirit of my question. Can't make a blast database with an alignment that way--the help flag doesn't specify such a method, at least. https://ibb.co/cSLNKF https://ibb.co/kmcf6v ...
written 10 days ago by jnf376940
0
votes
0
answers
99
views
0
answers
Alignment as BLAST-able database/other alignment avenues
... Hey all, I was wondering if there was a way to use an alignment as a local blast database. My problem is as follows: I have an old alignment of concatenated protein sequences that have CHARSET definitions defining the protein beginnings and endings at the bottom of the NEXUS file. Some folks doing ...
alignment nexus blast maftt written 10 days ago by jnf376940
0
votes
0
answers
183
views
0
answers
Comment: C: miR KEGG enrichment in Arabidopsis
... I did not need to do alignment or quality control of the sequencing data--it was handed off to me by a legacy researcher and I am more concerned with a qualitative assessment, rather than a quantitative one. I intend to go back and check his work after this to make sure we get the same results, but ...
written 6 months ago by jnf376940
0
votes
0
answers
183
views
0
answers
miR KEGG enrichment in Arabidopsis
... Hello all, I have a list of known miRNA's from an experiment in Arabidopsis (example: ath-MIR166a) and I am looking to find out what biochemical pathways they interact with, with KEGG or reactome.db preferably. I have preformed this analysis in humans several times with no issues. If anybody could p ...
enrichment arabidopsis mir kegg mirna written 6 months ago by jnf376940
4
votes
4
answers
265
views
5 follow
4
answers
Quick and Dirty Gene Network
... Hello all! I need to whip up a little network, preferably from known interactions, from a list of about 100 genes in Arabidopsis. All I have are the gene names. I don't care so much about up and down regulation right, just want to represent the genes interacting in one way or another--its more for d ...
arabidopsis network interactions gene network written 6 months ago by jnf376940 • updated 6 months ago by vakul.mohanty230
0
votes
0
answers
636
views
0
answers
Generating realistic ABI/AB1 electropherograms for educational purposes
... I was wondering if anyone knew of a method by which to generate electropherograms or abi/abi files for a lab I am teaching. The only reason why I am looking for a slightly more realistic way is because the lab is behind schedule due to some issues with the sequencer. I want the students to use softw ...
sequencing abi education ab1 electropherogram written 18 months ago by jnf376940
0
votes
1
answer
562
views
1
answers
Comment: C: Well-resolved Phylogenetic Dataset
... I have a followup question about the 109 E. coli ST131 strains. In the assemblies (ordered or not), there are multiple nodes per fasta file. Am I right in assuming that that means there are more than one contig per file (that is, the genome was not closed)? ...
written 18 months ago by jnf376940
3
votes
1
answer
562
views
1
answer
Well-resolved Phylogenetic Dataset
... Hello all, I am looking to test an alignment-free phylogenetic tree building algorithm I wrote. It can perform both gene and species trees. I have already tested it on a single gene primate tree, but I need some more data to further characterize the algorithm. I know there is a lot of data on TreeB ...
phylogeny dataset phylogenetics data written 18 months ago by jnf376940 • updated 18 months ago by kloetzl640
0
votes
0
answers
626
views
0
answers
OTU distances and assumptions
... I am working on a support vector machine doing some classification based on microbiomes. I am looking to take the relatedness of OTUs into account via some manner of distance measure, but it needs to be a single value. A distance matrix won't cut it. I have already proven to myself that, for an ingr ...
otu phylogenetics scoring distance clustering written 23 months ago by jnf376940

Latest awards to jnf3769

Scholar 23 months ago, created an answer that has been accepted. For A: RNA-seq normalization and differential expression

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1466 users visited in the last hour