User: kgbenn123

gravatar for kgbenn123
kgbenn12310
Reputation:
10
Status:
New User
Location:
Last seen:
1 year, 8 months ago
Joined:
3 years ago
Email:
k********@gmail.com

Posts by kgbenn123

<prev • 13 results • page 1 of 2 • next >
1
vote
1
answer
536
views
1
answer
Finding GO terms for an organism not in a GO database
... I'm trying to find the GO terms for my bacterium on AmiGO, but my organism is not listed in the species list. I've tried other websites with the same issue; any ideas as to what I'm doing wrong? ...
gene ncbi go terms amigo ontology written 20 months ago by kgbenn12310 • updated 20 months ago by pfs270
0
votes
2
answers
705
views
2
answers
Comment: C: Clustering program based on NJ phylogeny
... Phylip doesn't appear to have the function I'm looking for. I'm working with about 6000 seqs and want a program that can cluster through neighbor joining and output either a list of accessions that represent their respective clusters or some file format that allows me to extract them. ...
written 21 months ago by kgbenn12310
1
vote
2
answers
705
views
2
answers
Clustering program based on NJ phylogeny
... Does anyone have a recommendation for a clustering program that uses neighbor-joining phylogeny to cluster a dataset of protein sequences and output a representative from each cluster? I'm thinking of something that works like cdhit, but uses NJ instead of sequence identity for clustering. Any sugg ...
phylogeny nj protein clustering written 21 months ago by kgbenn12310 • updated 5 months ago by gbl170
1
vote
1
answer
542
views
1
answer
SNP discovery & genotyping in humans vs. flies
... I am led to believe that there are significant differences in how we discover and genotype SNPs from flies and humans, however I'm not sure why. I was told that the ability to create inbred lines of model organisms allows us to do a simpler version of SNP discovery than a population of humans. Can a ...
genotype snp sequencing written 21 months ago by kgbenn12310 • updated 21 months ago by Emily_Ensembl18k
0
votes
2
answers
1.7k
views
2
answers
Comment: C: Organism name from accession numbers
... I forgot to make this a reply to your comment so now there are two copies... Here are 29 numbers from one of the datasets I'm working with: ELW65244.1 XP_013802631.1 KYB28707.1 CRK95935.1 KHN78054.1 ENN75534.1 XP_017304189.1 XP_014597100.1 XP_006140718.1 XP_016061608.1 OBS71931.1 ELK375 ...
written 22 months ago by kgbenn12310
0
votes
2
answers
1.7k
views
2
answers
Comment: A: Organism name from accession numbers
... Here are 29 numbers from one of the datasets I'm working with: ELW65244.1 XP_013802631.1 KYB28707.1 CRK95935.1 KHN78054.1 ENN75534.1 XP_017304189.1 XP_014597100.1 XP_006140718.1 XP_016061608.1 OBS71931.1 ELK37553.1 XP_007099480.1 XP_006022987.1 XP_005633823.1 XP_008147166.1 KFO26429 ...
written 22 months ago by kgbenn12310
1
vote
2
answers
1.7k
views
2
answers
Organism name from accession numbers
... This seems like it may be well-worn territory, but I have many lists of protein accession numbers that are in text files in a column (from 330 to 20000 accession numbers). I would like to get the organism names for these proteins, but I'm not sure how. Any suggestions? Thanks ...
organism accession sequence numbers name written 22 months ago by kgbenn12310 • updated 22 months ago by Brian Bushnell16k
0
votes
0
answers
550
views
0
answers
Which profile search programs are best? Comparison studies?
... Is there any point in using HMMer over creating a PSSM of a motif and using PSI-BLAST? I can't find any significant, unbiased (Eddy publishes everything on HMMer performance) comparison studies on HMMer and its becoming difficult to justify using it from a literature review. ...
hmmer written 2.2 years ago by kgbenn12310
0
votes
1
answer
902
views
1
answers
Comment: C: Finding Organism Protein Databases
... I'm not even interested in any "specific" organisms, just a good cross-section of Domains. I totally agree though about RefSeq and UniProt. I think the problem is that they may not be the MOST up-to-date on physiology or...I have no idea. I'm just trying to put together diverse, quality seqs that I ...
written 2.5 years ago by kgbenn12310
0
votes
1
answer
902
views
1
answers
Comment: A: Finding Organism Protein Databases
... I have never used these (and I will give them both a shot tonight), but I assume I will still be going through every sequence to see if it is cited back to an organism-specific database? or do these have some feature that allows you to narrow your search that way? EDIT: Homologene was incredibly he ...
written 2.5 years ago by kgbenn12310

Latest awards to kgbenn123

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: 956 users visited in the last hour