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Forum: Bioinformatics 12-15-2015, 07:33 AM
Replies: 0
Views: 1,214
Posted By rdoan
String Protein-Protein Interactions

Hello,

Does String (http://string-db.org/) protein interaction analyses provide any information on the connectivity to a second list of genes?

For example,

If I provide a custom geneset for...
Forum: Bioinformatics 09-30-2014, 04:19 AM
Replies: 1
Views: 2,174
Posted By rdoan
Filter VCF using external Allele Frequency

Hello,
I would like to filter large multi-sample VCFs using allele frequencies obtained from VCFs or tab files from the EVS and 1000G datasets.

I know that GATK and VCFtools can filter for...
Forum: Bioinformatics 08-13-2014, 01:12 PM
Replies: 0
Views: 1,696
Posted By rdoan
Incorrect Phasing using Beagle 4

Hello, I am using beagle 4 to phase several thousand samples (>500 trios) plus some single samples. When using the ibd=true, gt=vcfin.vcf, ped=pedin.ped options without reference samples, the...
Forum: Bioinformatics 04-01-2014, 02:30 PM
Replies: 0
Views: 1,921
Posted By rdoan
PAML Error

I am running the aaml program of PAML using a amino acid alignment of several species. When I run the aaml.ctl file with my tree and phylip file, I receive the following error:

Error: initial...
Forum: Bioinformatics 12-31-2013, 10:08 AM
Replies: 0
Views: 1,409
Posted By rdoan
Prequel - PHAST

Hello, Is there a method to predict ancestral sequences using prequel on several thousand different sets of aligned sequences at one time without creating thousands of files and running each region...
Forum: Bioinformatics 12-27-2013, 09:35 AM
Replies: 0
Views: 2,297
Posted By rdoan
Site-wise Log-Likelihood

Hello,

I have several thousand sets of CDS from more 20 species. I would like to determine the Site-wise Log-Likelihood support for all amino acids for a given tree. Then I would like to compare...
Forum: Bioinformatics 12-24-2013, 11:37 AM
Replies: 1
Views: 2,713
Posted By rdoan
Pairwise alignment of multiple sequences

Hello, I would like to perform a pairwise alignment between 100 samples that each contain about 2,000 sequences from different genomic regions. What I would like is the percent identity (ID) at each...
Forum: Bioinformatics 09-03-2013, 08:35 AM
Replies: 1
Views: 1,820
Posted By rdoan
Probability of Occurence

How do I determine the if the overlap of genetic mutations, ex: copy number variants (CNVs) with a particular set of genomic regions is more than expected by random chance?

I have a subset of a...
Forum: Bioinformatics 10-12-2012, 01:34 PM
Replies: 1
Views: 1,560
Posted By rdoan
Nonsynonymous and Synonymous Sites in A Gene

Is it possible to predict the total possible synonymous and non-synonymous sites in a gene sequence? I would like a script where I can import a multi fasta file for several different genes and get...
Forum: Bioinformatics 10-12-2012, 07:17 AM
Replies: 0
Views: 1,841
Posted By rdoan
Create new Reference by merging SNV list with reference genome

Hello,

I would like to create incorporate a list of 5 million single base variants (SNVs) into an existing reference sequence resulting in a new reference that would match my genome of interest....
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